diff --git a/examples/HIV-1_latent.xml b/examples/HIV-1_latent.xml
new file mode 100644
index 0000000..f9fd745
--- /dev/null
+++ b/examples/HIV-1_latent.xml
@@ -0,0 +1,947 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/HIV-1_C.xml b/examples/HIV_models/HIV-1_C.xml
new file mode 100755
index 0000000..3f5178c
--- /dev/null
+++ b/examples/HIV_models/HIV-1_C.xml
@@ -0,0 +1,515 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- 
+				http://www.ncbi.nlm.nih.gov/nuccore/KC156214.1
+				sub type C full genome
+			-->
+			<length>9705</length>
+			<sequences>
+				CTGGAAGGGTTAATTTACTCCAAGAAAAGGCAAGACATCCTTGATTTGTGGGTTTATAACACACAAGGCTTCTTTCCTGATTGGCAAAACTACACACCGGGACCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTTCAAGCTAGTACCAGTTGACCCAAGGGAAGTAGAAGAAGCCAACGAAGGAGAAAACAACTGTCTGCTACACCCTATGAGCCAACATGGAATGGATGATGATCACAGAGAAGTATTAAAGTGGAAGTTTGACAGTCAACTAGCACACAAACACATGGCCCGCGAGCTACATCCGGAGTTTTACAAAGACTGCTGACACAAAAGGGACTTTCCGCTGGGACTTTCCACTTGGGCGTTCCAGGAGGTGGGGTCTGGGCGGGACCGGGGAGTGGCCAGCCCTCAGATGCTGCATATAAGCAGCTGCTTTTCGCCTGTACTGGGTCTCTCTAGGTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTGCCTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTCTAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCATTTTGGTTGCGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACTTGAAAGCGAAAGTAAGACCAGAGGAGATCTCTCGACGCAGGACTCGGCTTGCTGAAGTGCACTCGGCAAGAGGCGAGAGCGGCGACTGGTGAGTACGCCAATTTTATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTAGATAAATGGGAAAAAATTAGGTTAAGGCCAGGGGGAAAGAAAAAATATCAGCTAAAACACCTAGTATGGGCAAGCAGGGAGCTGGAAAAATTTGCACTTAACCCTGACCTTTTAGAAACATCAGAAGGCTGTAAACAAATAATAAGACAGCTACACCCAGCTCTCCAGACAGGAACAGAGGAACTCAAATCACTATATAACACAGTAGCAACTCTCTATTGTGTACATAAAAATATAGATGTGCGAGACACCAAGGAGGCCTTAGACAGGATAGAGGAGGAACAAAACAAATGTCAGCAAAAAACACAGCAGGCAGCAGCGGCTGACGGACAGGTCAGTCGAAATTTTCCTATAGTACAGAATCTTCAAGGGCAAATGGTACACCAGCCCTTATCACCTAGAACTTTGAATGCTTGGGTAAAAGTAGTAGAGGAGAAGGGTTTCAACCCAGAGGTAATACCCATGTTTACAGCATTATCAGAAGGAGCCACCCCACAAGATATGAACACTATGTTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATGAGGAGGCTGCAGAGTGGGATAGATTACATCCAGTACAGGCAGGGCCTGTTGCACCAGGCCAAATAAGGGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGCATGGATGACAAGTAACCCACCTGTTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGGTTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAAAACTTTAAGGGCTGAACAGGCTACACAAGATGTAAAAAATTGGATGACAGACACCCTGTTGGTCCAAAATGCGAACCCAGATTGCAAGACCATTTTAAGAGCACTAGGACCAGGGGCTACATTAGAGGAAATGATGACAGCATGTCAAGGAGTGGGAGGACCTAGCCACAAAGCAAGAGTGTTAGCCGAGGCAATGAGCCAAACAAACACAAACATACTGATGCAGAGAAGCAATTTCAAAGGCACTAGAAGAATTGTTAAATGTTTCAACTGTGGCAAGGAAGGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGACTGTACAGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCACAAGGGGAGGCCAGGGAATTTCCTTCAGAACAGGCCAGAGCCAACAGCCCCACCACTAGAACCAACAGCCCCACCAGCAGAGAGCTCCACCCCCGCTCTGAAGCAGGAGCAGAAAGACAGGGAACCCTCAATTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAATAAGAGTAGGGGGACAAATAAAGGAGGCTCTATTAGACACAGGAGCAGATGACACAGTATTAGAAGAATTAAGTTTGCCAGGAAAATGGAAACCAAAAATGATAGGAGGAATTGGAGGATTTATCAAAGTAAGACAGTATGATCAAATATCTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTATTGGTAGGACCTACACCTGTCAACATAATTGGAAGAAACATGTTGACTCAGCTTGGATGCACCCTAAATTTTCCAATTAGTCCCATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAGGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAACAGCAATTTGTGAAGAAATGGAAAAGGAAGGAAAAATTACAAAAATTGGGCCTGAAAACCCATATAACACTCCAGTATTTGCCATTAAAAAGAAGGACAGTACAAAGTGGAGAAAATTAGTAGATTTCAGGGAACTTAATAAAAGGACTCAAGACTTTTGGGAAGTTCAATTAGGAATACCACACCCAGCAGGGTTAAAAAAGAAAAAATCAGTGACAGTACTGGATGTGGGGGATGCATATTTTTCAGTTCCTTTAGATAAAGATTTCAGGAAATATACTGCATTCACCATACCTAGTATAAACAATGAAACACCAGGAATTAGATATCAATATAATGTGCTTCCACAAGGATGGAAAGGATCACCAGCAATATTCCAGAGTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAACCCAGAAATAGTCATCTATCAATATATGGATGACTTATATGTAGGGTCTGACTTAGAAATAGGGCAACATAGAGCAAAAATAGAGGAGTTAAGAAAACACCTATTGAAATGGGGATTTACCACACCAGACAAGAAACATCAGAAGGAGCCCCCATTTCTTTGGATGGGGTATGAACTCCATCCTGACAAATGGACAGTACAGTCTATACAGCTACCGGAAAAGGACAGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAACTGGGCAAGTCAGATTTACCCAGGAATTAAAGTAAAGCAAATGTGTAAACTCCTTAGGGGAGCCAAAGCACTAACAGATGTAGTACCACTGACTGAAGAAGCAGAATTAGAATTGGCAGAGAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAGGGAGATGACCAGTGGACATATCAAATTTACCAAGAACCATTCAAAAATCTAAAAACAGGAAAATATGCAAAACAGAGAACTGCCCACACAAATGATGTAAAACAATTAACTGAGGCAGTGCAGAAAATATGCATGGAAAGCATAGTAATATGGGGGAAGATTCCTAAGTTTAGACTACCCATCCAAAAGGAAACATGGGAGACATGGTGGACAGACTACTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTATTAATACCCCTCCCCTAGTAAAATTATGGTATCAGCTGGAGAAGGAACCCATAGCAGGGGCAGAAACTTTCTATGTAGATGGAGCAGCTAATAGGGAAACTAAAAAGGGAAAAGCAGGTTATGTTACTGACAGAGGAAGGCAGAAAGTTGTTTCTCTAACTGGAACAACAAATCAAAAGACTGAGTTACAAGCAATTCAGCTAGCTTTGCAAGACTCAGGATCAGAAGTAAATATAGTAACAGACTCACAGTATGCATTAGGAATCATTCAAGCACAACCAGATAAGAGTGAATCAGAGTTAGTCAATCAAATAATAGAACAGCTAATAAAAAAGGAAAGAATCTACCTGTCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTAAGTAGTGGAATCAGGAAAGTACTGTTTCTAGATGGAATAGATAAAGCTCAAGAAGACCATGAAAGATATCACAGCAATTGGAGAGCGATGGCTAGCGAGTTTAATCTGCCACCCATAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGGGAAGCCATACATGGACAAGTAGACTGTAGTCCAGGGGTATGGCAACTAGATTGTACACACTTAGAAGGGAAAATCATCCTGGTAGCAGTCCATGTAGCCAGTGGATACATAGAAGCAGAAGTCATCCCAACAGAAACAGGACAAGAAACAGCATACTATATACTAAAATTAGCAGGAAGATGGCCAGTCAAAGTAATACATACAGACAATGGCCCTAATTTTACCAGTGCTGCAGTTAAGGCAGCCTGTTGGTGGGCAGGTATCCAACAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAGGGAGTAGTGGAATCCATGAATAAAGAATTAAAGAAAATCATAGGGCAAGTAAGAGATCAAGCTGAGCACCTTAAGACAGCAGTACAAATGGCAGTGTTCATTCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACACTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAAGCAATTACAAAAACAAATTATAAAAATTCAAAATTTTCGGGTTTATTACAGAGACAGCAGAGATCCAATTTGGAAAGGACCAGCCAAACTACTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAACAGTGACATAAAGGTAGTACCAAGAAGGAAAGCAAAGATTATTAAGGACTATGGAAAACAGATGGCAGGTGCTGATTGTGTGGCAGGTAGACAGGATGAAGATTAGAACATGGAATAGTCTAGTAAAGCACCATATGTATGTTTCAAGGAGAGCTGATGGATGGTTTTACAGACATCACTATGAAAGCAGACATCCAAAAATAAGTTCAGAAGTACACATCCCATTAGGGGATGCTAGATTAGTAATAAAAACATATTGGGGTTTGCAGACAGGAGAAAGAGCTTGGCATTTGGGTCATGGAGTCTCCATAGAATGGAGACTGAAAAGATATAGCACACAAGTAGACCCTGACCTGGCAGATCAACTAATTCATATGCATTATTTTGATTGTTTTGCAGACTCTGCCATAAGACAAGCCATACTAGGACACGTAGTTAGCCCTAGGTGTGACTATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTGACAGCATTGATAAAGCCAAAAAAGATAAAGCCACCTCTGCCTAGTGTTAGCAAGTTAGTAGAGGATAAATGGAACAAGCCCCAGAAGACCAGGGGCCGCAGAGGGAACCATACAATGAATGGACACTAGAGCTTCTAGAGGAACTCAAGCAGGAAGCTGTCAGACACTTTCCTAGGCCATGGCTTCACAGTTTAGGACAACATATCTATGAAACCTATGGGGACACTTGGACGGGAGTTGAAGCCATAATAAGAATTCTGCAACAACTGTTGTTTGTTCATTTCAGAATTGGGTGCCAGCATAGCAGAATAGGCATTATACGACAGAGAAGAGCAAGAAATGGAGCCAATAGATCCTAAACTAGAGCCCTGGAATCATCCAGGAAGCCAGCCTAAGACTGCTTGTAATAAGTGCTATTGTAAAAAATGTAGCTATCATTGTCTAGTTTGCTTTCAGACAAAAGGCTTAGGCATTTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGCGCTCCTCCAAGCAGTAAGGATCATCAAAATCCTCTACCAAAGCAGTAAGTATATGTAATGTTAGACTTAGTAGCAAGAGTAGATTATAGAATAGGAGTAGGAGCATTAATAGTAGCACTAATCATAGCAATAGTTGTGTGGATCCTAGCATATATAGAATATAAAAGGTGGTTAAAACAAAAGAAAATAGACTGGTTAATTAAAAGAATTAGGGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAGGGGGATACAGAGGAATTATCAACAATGGTGGATATGGAGCATCTTGGCCTTTTGGATGTTAATGGTTAGTGTGAGGGGAAACTTGTGGGTTACAGTCTATTATGGGGTACCTGTGTGGAAAGAAGCAAAAACTACTCTATTCTGTGCATCAGATGCTAAAGCATATGACAAGGAAGTGCATAATGTCTGGGCTACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAATAAAATTGGAAAATGTAACAGAAAATTTTAATATGTGGAAAAATGATATGGTGGATCAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTGAAGTTGACCCCACTTTGTGTCACTTTAAACTGTAGTCATAATATTACGGTTAATGGTACCATGGGAAATGGTACCAGGGGAAATGATAGTACGATTGGGAAAATGGGAGATGAAATGACAAATTGCTCTTTCAATGCAACCACAGAAATAAAAGATAAGAAAAAGCTAGAATATGCACTTTTTTATAAACTTGATGTAGTAACACTTGAGGAAAACTCCAGTGAGTACAGATTAATAAATTGTAATACCTCAGTAGTTACACAAGCCTGTCCAAAGGTTTCGTTTCACCCAATTCCTATACATTATTGTGCTCCTGCTGGTTATGCGATTCTAAAGTGTAATAATAAGACATTCAATGGAACAGGACCATGCAATAAGATCAGCACTGTACAGTGTACACATGGGATCAAGCCAGTGGTATCTACTCAACTACTGTTAAATGGTAGTCTAGCAGAAAAAGAGATAATAGTTAGATCTGAAAATATACAGGACAATGTCAAAACAATCATAGTACATCTTAATGAATCTGTGAAAATTGAGTGTACAAGGCCCGGCAATAATACAAGAAAAAGTGTGAGGATAGGACCAGGACAAACATTCTTTGCAACAGGAGACATAATAGGAGATATAAGACAAGCATACTGTACCATTAATGGGACTCAATGGAATGACACTTTAAATAGGGTAAGAGAAACATTACAAAGGCACTTCCCTAATAAAACAATAAAATTTAGACCACACTCAGGAGGGGACTTAGAAATTACAACACATAGCTTTAATTGTAGAGGAGAGTTTTTCTATTGCAATACATCAAAAATATTTGATAGTGACAATGCAAACAAAACTTCAGGAAATATCACACTCCCATGCAAAATAAAACAAATCATAAACATGTGGCAGGGGGTAGGAAGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTACATCAAATATCACAGGACTACTATTGACACGTGATGGAGGCAATGTTACAAATGACACAGAGATATTCAGACCTGGAGGAGGAAATATGAGGGACAATTGGAGAAGTGAATTATACAAATATAAAGTGGTAGAAATTAAGCCATTAGGGATAGCACCCACCAAGGCAAAAAGGCGAGTGGTGGAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTGTATTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATAGCGCTGACGGTACAGGCCAGACAATTGTTGTCTGGTATAGTGCAACAGCAAAACAATTTGCTGAGAGCTATAGAGGCGCAACAGCATATGTTGCAACTCACGGTCTGGGGCATTAAACAGCTCCAGGCAAGAGTCCTGGCTATAGAAAGATACCTAGAGGATCAACAGCTCCTAGGGATTTGGGGCTGCTCTGGAAAACTCATCTGCACCACTGCCGTGCCTTGGAACAATAGTTGGAGTAATAAATCTCAAGATGATATTTGGGGCAATATGACCTGGATGCAATGGGACAGAGAAATTAGCAATTACACAGACACAATATACAGGTTGCTTGAAGACTCGCAAATCCAGCAGGAAAAGAATGAAAAGGATTTACTAGCATTGGACAGTTGGCAAAATTTGTGGAATTGGTTTAACATAACAAAATGGCTGTGGTATATAAAAATATTCATAATGATAGTAGGAGGCTTAATAGGTTTAAGAATAATTTTTGCTGTACTATCTATAGTAAATAGAGTTAGGCAGGGATACTCACCTTTGTCGTTTCAGACCCTTATCCCAAACCAGAGGGAACCCGACAGGCTCGGAAGAATCGAAGAAGAAGGTGGAGAGCCAGACAGAAACAGATCCATTCGATTGGTGAACGGATTCTTAGCTCTTACCTGGGACGACCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGATTGAGAGACTTCATATTGGTGACAGTGAGAGTGGTGGAACTTCTGGGACGCAGCAGCTTCAGGGGACTACAGAGGGGGTGGGAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAGTATTGGGGTCTAGAGCTAAAAAAGAGTGCTATTAGTTTGCTTGATACCACAGCAATAGCAGTAGCTGAAGGAACAGATAGGATTATAGAATTCCTACAGAGAATTTGTAGAGCTATCTACCATATACCTAGAAGAATAAGACAGGGCTTTGAAGCAGCTTTGCAATAAAATGGGGGGCAAGTGGTCAAAAAGCAGTATAGTTGGATGGCCTAATGTAAGGGAAAGAATAAGGCGAACTGATCCAGCAGCAGAGGGAGTAGGAGCAGCATCTCGAGACTTAGAGAGACATGGGGCACTTACTACCAGCAACACAGTCAGCAACAATGCTGCATGTGCCTGGCTGGAAGCACAAGAAGAGGAAAAAGAAGTAGGCTTTCCAGTCAGACCTCAAGTGCCTTTAAGACCAATGACTTATAAAGGAGCATTCGATCTCAGCTTCTTTTTAAAAGAAAAGGGGGGACTGGAAGGGTTAATTTACTCCAAGAAAAGGCAAGACATCCTTGATTTGTGGGTTTATAACACACAAGGCTTCTTTCCTGATTGGCAAAACTACACACCGGGACCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTTCAAGCTAGTACCAGTTGACCCAAGGGAAGTAGAAGAAGCCAACGAAGGAGAAAACAACTGTCTGCTACACCCTATGAGCCAACATGGAATGGATGATGATCACAGAGAAGTATTAAAGTGGAAGTTTGACAGTCAACTAGCACACAAACACATGGCCCGCGAGCTACATCCGGAGTTTTACAAAGACTGCTGACACAAAAGGGACTTTCCGCTGGGACTTTCCACTTGGGCGTTCCAGGAGGTGGGGTCTGGGCGGGACCGGGGAGTGGCCAGCCCTCAGATGCTGCATATAAGCAGCTGCTTTTCGCCTGTACTGGGTCTCTCTAGGTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTGCCTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTCTAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCATTTTGGTTGCGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>792-2270</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2072-5074</coordinates>
+			</feature>
+			
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5022-5597</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6039-6293</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6217-8775</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8780-9400</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-492</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1000</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-191</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-84</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-852</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/activegrowth_high.xml b/examples/HIV_models/activegrowth_high.xml
new file mode 100755
index 0000000..50620f0
--- /dev/null
+++ b/examples/HIV_models/activegrowth_high.xml
@@ -0,0 +1,947 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>500</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/activegrowth_low.xml b/examples/HIV_models/activegrowth_low.xml
new file mode 100755
index 0000000..059d686
--- /dev/null
+++ b/examples/HIV_models/activegrowth_low.xml
@@ -0,0 +1,947 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>5</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/fitness_hla.xml b/examples/HIV_models/fitness_hla.xml
new file mode 100755
index 0000000..9a129eb
--- /dev/null
+++ b/examples/HIV_models/fitness_hla.xml
@@ -0,0 +1,2114 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+			#	HLA: A*01-B*08-DRB1*04:01 most common in USA causcasians (doi:10.1016/j.humimm.2007.10.009)
+			#	B*08: fitness based on doi:10.1371/journal.pone.0006687
+			#	A*01: fitness based on doi:10.1371/journal.pone.0006687
+			-->
+
+			<empiricalFitness id="GAG26">
+				<feature>gag</feature>
+				<sites>26</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.01 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="GAG65">
+				<feature>gag</feature>
+				<sites>65</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					0.99 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="GAG76A">
+				<feature>gag</feature>
+				<sites>76</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.02 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					0.99 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="GAG79A">
+				<feature>gag</feature>
+				<sites>79</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.02 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					0.98 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="GAG81">
+				<feature>gag</feature>
+				<sites>81</sites>
+				<values>
+					0.99 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="GAG104">
+				<feature>gag</feature>
+				<sites>104</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.01 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="GAG268">
+				<feature>gag</feature>
+				<sites>268</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.02 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					0.98 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="GAG331">
+				<feature>gag</feature>
+				<sites>331</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					0.98 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.02 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="GAG390">
+				<feature>gag</feature>
+				<sites>390</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.01 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="GAG439A">
+				<feature>gag</feature>
+				<sites>439</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.01 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					0.99 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="GAG470A">
+				<feature>gag</feature>
+				<sites>470</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.01 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="GAG479">
+				<feature>gag</feature>
+				<sites>479</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.01 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="RT200">
+				<feature>RT</feature>
+				<sites>200</sites>
+				<values>
+					0.98 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="RT275">
+				<feature>RT</feature>
+				<sites>275</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.02 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="RT288A">
+				<feature>RT</feature>
+				<sites>288</sites>
+				<values>
+					1.02 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="RT454">
+				<feature>RT</feature>
+				<sites>454</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.02 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					0.98 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="RT461">
+				<feature>RT</feature>
+				<sites>461</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.02 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					0.98 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="RT466">
+				<feature>RT</feature>
+				<sites>466</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					0.98 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="RT468">
+				<feature>RT</feature>
+				<sites>468</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.02 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					0.98 <!-- S -->
+					1.01 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="RT469">
+				<feature>RT</feature>
+				<sites>469</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.02 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="IN91A">
+				<feature>IN</feature>
+				<sites>91</sites>
+				<values>
+					1.01 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="IN119A">
+				<feature>IN</feature>
+				<sites>119</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					0.99 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="IN138">
+				<feature>IN</feature>
+				<sites>138</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					0.99 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="IN173">
+				<feature>IN</feature>
+				<sites>173</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					0.98 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.02 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="IN218">
+				<feature>IN</feature>
+				<sites>218</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					0.99 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA18">
+				<feature>NEF</feature>
+				<sites>18</sites>
+				<values>
+					1.01 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					0.99 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA18A">
+				<feature>NEF</feature>
+				<sites>18</sites>
+				<values>
+					1.01 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA23A">
+				<feature>NEF</feature>
+				<sites>23</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					0.99 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA40">
+				<feature>NEF</feature>
+				<sites>40</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					0.99 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.01 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA83">
+				<feature>NEF</feature>
+				<sites>83</sites>
+				<values>
+					1.01 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA87">
+				<feature>NEF</feature>
+				<sites>87</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.01 <!-- I -->
+					1.00 <!-- K -->
+					0.99 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA91">
+				<feature>NEF</feature>
+				<sites>91</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.01 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA93">
+				<feature>NEF</feature>
+				<sites>93</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					0.99 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.01 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA94">
+				<feature>NEF</feature>
+				<sites>94</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.02 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					0.98 <!-- K -->
+					1.00 <!-- L -->
+					1.02 <!-- M -->
+					1.02 <!-- N -->
+					1.00 <!-- P -->
+					1.02 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.01 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA94A">
+				<feature>NEF</feature>
+				<sites>94</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					0.99 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA101">
+				<feature>NEF</feature>
+				<sites>101</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.02 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					0.98 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA104">
+				<feature>NEF</feature>
+				<sites>104</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.01 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA105">
+				<feature>NEF</feature>
+				<sites>105</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					0.98 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.02 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA170">
+				<feature>NEF</feature>
+				<sites>170</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.01 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA182A">
+				<feature>NEF</feature>
+				<sites>182</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.01 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA188A">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					0.99 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA192">
+				<feature>NEF</feature>
+				<sites>192</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.01 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF_HLA194">
+				<feature>NEF</feature>
+				<sites>194</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.02 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					0.98 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/fitness_none.xml b/examples/HIV_models/fitness_none.xml
new file mode 100755
index 0000000..8ae10ec
--- /dev/null
+++ b/examples/HIV_models/fitness_none.xml
@@ -0,0 +1,237 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/indel.xml b/examples/HIV_models/indel.xml
new file mode 100755
index 0000000..d9875e9
--- /dev/null
+++ b/examples/HIV_models/indel.xml
@@ -0,0 +1,242 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			
+					<!-- suggested from doi:10.1093/ve/vez022 -->
+			        <indelmodel model="NB">0.08 1</indelmodel>
+					<insertprob>6E-4<!--3.5E-4--></insertprob>
+					<deleteprob>6E-4<!--3.5E-4--></deleteprob>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/latencydeath_high.xml b/examples/HIV_models/latencydeath_high.xml
new file mode 100755
index 0000000..34f93b6
--- /dev/null
+++ b/examples/HIV_models/latencydeath_high.xml
@@ -0,0 +1,947 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0084</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/latencydeath_low.xml b/examples/HIV_models/latencydeath_low.xml
new file mode 100755
index 0000000..f2743c8
--- /dev/null
+++ b/examples/HIV_models/latencydeath_low.xml
@@ -0,0 +1,947 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.00373</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/latencygrowth_high.xml b/examples/HIV_models/latencygrowth_high.xml
new file mode 100755
index 0000000..9589777
--- /dev/null
+++ b/examples/HIV_models/latencygrowth_high.xml
@@ -0,0 +1,947 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.0045</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/latencygrowth_low.xml b/examples/HIV_models/latencygrowth_low.xml
new file mode 100755
index 0000000..bd910fd
--- /dev/null
+++ b/examples/HIV_models/latencygrowth_low.xml
@@ -0,0 +1,947 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.002</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/latencyrate_high.xml b/examples/HIV_models/latencyrate_high.xml
new file mode 100755
index 0000000..fb89782
--- /dev/null
+++ b/examples/HIV_models/latencyrate_high.xml
@@ -0,0 +1,947 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0052 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/latencyrate_low.xml b/examples/HIV_models/latencyrate_low.xml
new file mode 100755
index 0000000..df67b36
--- /dev/null
+++ b/examples/HIV_models/latencyrate_low.xml
@@ -0,0 +1,947 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0013 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/mutrate_high.xml b/examples/HIV_models/mutrate_high.xml
new file mode 100755
index 0000000..bd8df2a
--- /dev/null
+++ b/examples/HIV_models/mutrate_high.xml
@@ -0,0 +1,947 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-4</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/mutrate_low.xml b/examples/HIV_models/mutrate_low.xml
new file mode 100755
index 0000000..b2bd24d
--- /dev/null
+++ b/examples/HIV_models/mutrate_low.xml
@@ -0,0 +1,947 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-6</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/reactivation_high.xml b/examples/HIV_models/reactivation_high.xml
new file mode 100755
index 0000000..848d70b
--- /dev/null
+++ b/examples/HIV_models/reactivation_high.xml
@@ -0,0 +1,947 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00216 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/reactivation_low.xml b/examples/HIV_models/reactivation_low.xml
new file mode 100755
index 0000000..bc15bef
--- /dev/null
+++ b/examples/HIV_models/reactivation_low.xml
@@ -0,0 +1,947 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00054 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/recomb.xml b/examples/HIV_models/recomb.xml
new file mode 100755
index 0000000..670907a
--- /dev/null
+++ b/examples/HIV_models/recomb.xml
@@ -0,0 +1,951 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>200000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+		
+		<!-- suggested from doi:10.1371/journal.pcbi.1000660 -->
+		<replicator>
+			<recombinantReplicator>
+				<dualInfectionProbability>0.07</dualInfectionProbability>
+				<recombinationProbability>1.4E-5</recombinationProbability>
+			</recombinantReplicator>	
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/size_1.xml b/examples/HIV_models/size_1.xml
new file mode 100755
index 0000000..c03c640
--- /dev/null
+++ b/examples/HIV_models/size_1.xml
@@ -0,0 +1,947 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>1</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/examples/HIV_models/size_100.xml b/examples/HIV_models/size_100.xml
new file mode 100755
index 0000000..e1d387c
--- /dev/null
+++ b/examples/HIV_models/size_100.xml
@@ -0,0 +1,947 @@
+<santa xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:noNamespaceSchemaLocation="santa.xsd">
+	<replicates>1</replicates>
+	<simulation>
+		<!--
+		#	rate plasma -> latent (doi:10.1371/journal.pcbi.1000533)
+		#	rate latent -> plasma chosen to make reservoir half-life 70 weeks (doi:10.1086/428777)
+		-->
+		<transferRates>0 0.0026 0.00108 0</transferRates>
+		<genome>
+			<!-- http://www.ncbi.nlm.nih.gov/nuccore/K03455.1
+				 premature stop codon in NEF replaced with TGG
+				 premature start codon in vpu replaced with ATG
+			-->
+			<length>9719</length>
+			<sequences>
+				TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+			</sequences>
+			
+			<feature>
+				<name>gag</name>
+				<type>aminoAcid</type>
+				<coordinates>790-2289</coordinates>
+			</feature>
+
+			<feature>
+				<name>pol</name>
+				<type>aminoAcid</type>
+				<coordinates>2085-5093</coordinates>
+			</feature>
+			
+			<feature>
+				<name>PR</name>
+				<type>aminoAcid</type>
+				<coordinates>2253-2549</coordinates>
+			</feature>
+			<feature>
+				<name>RT</name>
+				<type>aminoAcid</type>
+				<coordinates>2550-4229</coordinates>
+			</feature>
+			<feature>
+				<name>IN</name>
+				<type>aminoAcid</type>
+				<coordinates>4230-5093</coordinates>
+			</feature>
+
+			<feature>
+				<name>vif</name>
+				<type>aminoAcid</type>
+				<coordinates>5041-5616</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpr</name>
+				<type>aminoAcid</type>
+				<coordinates>5559-5847</coordinates>
+			</feature>
+
+			<feature>
+				<name>vpu</name>
+				<type>aminoAcid</type>
+				<coordinates>6062-6307</coordinates>
+			</feature>
+
+			<feature>
+				<name>env</name>
+				<type>aminoAcid</type>
+				<coordinates>6225-8792</coordinates>
+			</feature>
+
+			<feature>
+				<name>NEF</name>
+				<type>aminoAcid</type>
+				<coordinates>8797-9414</coordinates>
+			</feature>
+		</genome>
+		
+		<compartment>
+			<name>plasma</name>
+
+		<fitnessFunction>
+			<!--
+				start and stop codon
+			-->
+			
+			<empiricalFitness id="gagstop">
+				<feature>gag</feature>
+				<sites>1-500</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+						
+			<empiricalFitness id="gag1">
+				<feature>gag</feature>
+				<sites>1</sites>
+				<values>
+                        0.001 <!-- A -->
+                        0.001 <!-- C -->
+                        0.001 <!-- D -->
+                        0.001 <!-- E -->
+                        0.001 <!-- F -->
+                        0.001 <!-- G -->
+                        0.001 <!-- H -->
+                        0.001 <!-- I -->
+                        0.001 <!-- K -->
+                        0.001 <!-- L -->
+                        1.00 <!-- M -->
+                        0.001 <!-- N -->
+                        0.001 <!-- P -->
+                        0.001 <!-- Q -->
+                        0.001 <!-- R -->
+                        0.001 <!-- S -->
+                        0.001 <!-- T -->
+                        0.001 <!-- V -->
+                        0.001 <!-- W -->
+                        0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="polstop">
+				<feature>pol</feature>
+				<sites>1-1003</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vifstop">
+				<feature>vif</feature>
+				<sites>1-192</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vif1">
+				<feature>vif</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpustop">
+				<feature>vpu</feature>
+				<sites>1-82</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="vpu1">
+				<feature>vpu</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="envstop">
+				<feature>env</feature>
+				<sites>1-856</sites>
+				<values>
+					1.00 <!-- A -->
+					1.00 <!-- C -->
+					1.00 <!-- D -->
+					1.00 <!-- E -->
+					1.00 <!-- F -->
+					1.00 <!-- G -->
+					1.00 <!-- H -->
+					1.00 <!-- I -->
+					1.00 <!-- K -->
+					1.00 <!-- L -->
+					1.00 <!-- M -->
+					1.00 <!-- N -->
+					1.00 <!-- P -->
+					1.00 <!-- Q -->
+					1.00 <!-- R -->
+					1.00 <!-- S -->
+					1.00 <!-- T -->
+					1.00 <!-- V -->
+					1.00 <!-- W -->
+					1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="env1">
+				<feature>env</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEFstop">
+				<feature>NEF</feature>
+				<sites>1-206</sites>
+				<values>
+                        1.00 <!-- A -->
+                        1.00 <!-- C -->
+                        1.00 <!-- D -->
+                        1.00 <!-- E -->
+                        1.00 <!-- F -->
+                        1.00 <!-- G -->
+                        1.00 <!-- H -->
+                        1.00 <!-- I -->
+                        1.00 <!-- K -->
+                        1.00 <!-- L -->
+                        1.00 <!-- M -->
+                        1.00 <!-- N -->
+                        1.00 <!-- P -->
+                        1.00 <!-- Q -->
+                        1.00 <!-- R -->
+                        1.00 <!-- S -->
+                        1.00 <!-- T -->
+                        1.00 <!-- V -->
+                        1.00 <!-- W -->
+                        1.00 <!-- Y -->
+				</values>
+			</empiricalFitness>
+			
+			<empiricalFitness id="NEF1">
+				<feature>NEF</feature>
+				<sites>1</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					1.00 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<!--
+				nef replication capacity (CD4 down-modulation and HLA-I down-modulation) 
+				doi: 10.1093/ve/vez029
+			-->
+			
+			<empiricalFitness id="NEF21">
+				<feature>NEF</feature>
+				<sites>21</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					1.464 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.515 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF28">
+				<feature>NEF</feature>
+				<sites>28</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.851 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF33">
+				<feature>NEF</feature>
+				<sites>33</sites>
+				<values>
+					1.293 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF43">
+				<feature>NEF</feature>
+				<sites>43</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.694 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF57">
+				<feature>NEF</feature>
+				<sites>57</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.009 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.008 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					1.000 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF71">
+				<feature>NEF</feature>
+				<sites>71</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.854 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF76">
+				<feature>NEF</feature>
+				<sites>76</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.843 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF80">
+				<feature>NEF</feature>
+				<sites>80</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.186 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.832 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					1.000 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF88">
+				<feature>NEF</feature>
+				<sites>88</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.870 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					1.000 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF102">
+				<feature>NEF</feature>
+				<sites>102</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.466 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.754 <!-- W --> <!-- wildtype? -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF123">
+				<feature>NEF</feature>
+				<sites>123</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					1.000 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.064 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF133">
+				<feature>NEF</feature>
+				<sites>133</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					1.000 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.599 <!-- T -->
+					1.000 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF135">
+				<feature>NEF</feature>
+				<sites>135</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.135 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					1.000 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF143">
+				<feature>NEF</feature>
+				<sites>143</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					1.000 <!-- F -->
+					0.001 <!-- G -->
+					0.001 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					0.001 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					0.001 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.941 <!-- Y -->
+				</values>
+			</empiricalFitness>
+
+			<empiricalFitness id="NEF188">
+				<feature>NEF</feature>
+				<sites>188</sites>
+				<values>
+					0.001 <!-- A -->
+					0.001 <!-- C -->
+					0.001 <!-- D -->
+					0.001 <!-- E -->
+					0.001 <!-- F -->
+					0.001 <!-- G -->
+					0.689 <!-- H -->
+					0.001 <!-- I -->
+					0.001 <!-- K -->
+					1.000 <!-- L -->
+					0.001 <!-- M -->
+					0.001 <!-- N -->
+					0.001 <!-- P -->
+					0.001 <!-- Q -->
+					1.000 <!-- R -->
+					0.001 <!-- S -->
+					0.001 <!-- T -->
+					0.001 <!-- V -->
+					0.001 <!-- W -->
+					0.001 <!-- Y -->
+				</values>
+			</empiricalFitness>
+		</fitnessFunction>
+
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>10</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<growthModel>
+			<!--
+			# growth rate based on Figure 1B from 10.1128/JVI.02520-15
+			# 10^5 virions in 1 ml of plasma
+			-->
+			<growthRate>50</growthRate>
+			<carryingPopulation>100000</carryingPopulation>
+		</growthModel>
+
+		<mutator>
+			<nucleotideMutator>
+				<!-- from doi:10.1371/journal.pbio.1002251 -->
+				<mutationRate>9.3E-5</mutationRate>
+				<rateBias>
+	                    0.42 2.49 0.29
+	                    1.73 0.23 4.73
+	                    6.99 0.20 0.60
+	                    1.02 2.56 0.88
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+			
+		<replicator>
+			<clonalReplicator />		
+		</replicator>
+
+		<!-- ten years (1 cycle per 2.6 days) doi:10.1126/science.271.5255.1582 -->
+		<epoch>
+			<name>active</name>
+			<generationCount>1400</generationCount>
+		</epoch>
+		
+		<epoch>
+			<name>treatment</name>
+			<generationCount>1400</generationCount>
+			
+			<fitnessFunction>
+				<noFitness>
+				</noFitness>
+			</fitnessFunction>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atFrequency>140</atFrequency>
+				<fileName>alignment_plasma.fasta</fileName>
+				<alignment>
+					<sampleSize>100</sampleSize>
+					<format>FASTA</format>
+					<label>plasma_%s_%g</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+		
+		<compartment>
+		<name>latent_reservoir</name>
+		
+		<populationType>dynamicPopulation</populationType>
+		
+		<population>
+			<populationSize>0</populationSize>
+			<inoculum>all</inoculum>
+		</population>
+		
+		<!--
+		# proloferation (doi:10.1002/eji.200323763)
+		# death-birth 0.001 day-1 (doi:10.1371/journal.pcbi.1000533)
+		-->
+		<growthModel>
+			<split>0.003</split>
+			<death>0.0056</death>
+		</growthModel>
+		
+		<fitnessFunction></fitnessFunction>
+
+		<mutator>
+			<nucleotideMutator>
+				<mutationRate>0.0</mutationRate>
+				<rateBias>
+	                   0 0 0 0
+	                   0 0 0 0
+	                   0 0 0 0
+	                </rateBias>
+			</nucleotideMutator>
+		</mutator>
+
+		<replicator>
+			<clonalReplicator></clonalReplicator>
+		</replicator>
+
+		<epoch>
+			<name>epoch</name>
+			<generationCount>2800</generationCount>
+		</epoch>
+		
+		<samplingSchedule>
+			<sampler>
+				<atGeneration>1680</atGeneration>
+				<fileName>alignment_latent_1680.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>1960</atGeneration>
+				<fileName>alignment_latent_1960.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2240</atGeneration>
+				<fileName>alignment_latent_2240.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2520</atGeneration>
+				<fileName>alignment_latent_2520.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+			<sampler>
+				<atGeneration>2800</atGeneration>
+				<fileName>alignment_latent_2800.fasta</fileName>
+				<alignment>
+					<sampleSize>10</sampleSize>
+					<format>FASTA</format>
+					<label>latent_%s_%g_%a</label>
+				</alignment>
+			</sampler>
+		</samplingSchedule>
+		</compartment>
+	</simulation>
+</santa>
diff --git a/src/santa/simulator/NegBinIndelModel.java b/src/santa/simulator/NegBinIndelModel.java
index 28a8643..3fa253f 100644
--- a/src/santa/simulator/NegBinIndelModel.java
+++ b/src/santa/simulator/NegBinIndelModel.java
@@ -1,7 +1,6 @@
 
 package santa.simulator;
 
-import santa.simulator.Random;
 import org.apache.commons.math3.distribution.PascalDistribution;
 
 public class NegBinIndelModel extends IndelModel {
diff --git a/src/santa/simulator/Random.java b/src/santa/simulator/Random.java
index a9d1270..7471469 100644
--- a/src/santa/simulator/Random.java
+++ b/src/santa/simulator/Random.java
@@ -1,6 +1,10 @@
 package santa.simulator;
 
 import java.util.Collection;
+import java.util.List;
+import java.util.Collections;
+import java.util.ListIterator;
+import java.util.RandomAccess;
 
 import org.apache.commons.math3.random.RandomDataGenerator;
 
@@ -38,6 +42,10 @@ public static int[] nextPermutation(int i, int i1) {
     public static long nextPoisson(double v) {
         return randomData.nextPoisson(v);
     }
+    
+    public static int nextBinomial(int n, double p) {
+        return randomData.nextBinomial(n, p);
+    }
 
     public static Object[] nextSample(Collection<?> collection, int i) {
         return randomData.nextSample(collection, i);
@@ -70,6 +78,42 @@ public static void shuffle(int[] numbers) {
         }
     }
     
+    // From java.util.Collections
+    // Added so that all random calls go through this class
+    public static void shuffle(List<?> list) {
+        int size = list.size();
+        if (size < 5000 || list instanceof RandomAccess) {
+            for (int i=size; i>1; i--)
+                Collections.swap(list, i-1, nextInt(0, i - 1));
+        } else {
+            Object arr[] = list.toArray();
+
+            // Shuffle array
+            for (int i=size; i>1; i--)
+                swap(arr, i-1, nextInt(0, i - 1));
+
+            // Dump array back into list
+            // instead of using a raw type here, it's possible to capture
+            // the wildcard but it will require a call to a supplementary
+            // private method
+            ListIterator it = list.listIterator();
+            for (int i=0; i<arr.length; i++) {
+                it.next();
+                it.set(arr[i]);
+            }
+        }
+    }
+    
+    /**
+     * From java.util.Collections
+     * Swaps the two specified elements in the specified array.
+     */
+    private static void swap(Object[] arr, int i, int j) {
+        Object tmp = arr[i];
+        arr[i] = arr[j];
+        arr[j] = tmp;
+    }
+    
     public static void setSeed(long seed) {
     	((RandomDataGenerator) randomData).reSeed(seed);
     }
diff --git a/src/santa/simulator/Simulation.java b/src/santa/simulator/Simulation.java
index 083b722..4579b8f 100644
--- a/src/santa/simulator/Simulation.java
+++ b/src/santa/simulator/Simulation.java
@@ -1,17 +1,11 @@
 package santa.simulator;
 
+import santa.simulator.compartments.CompartmentEpoch;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.logging.Logger;
-
-import santa.simulator.genomes.GenePool;
-import santa.simulator.genomes.GenomeDescription;
-import santa.simulator.genomes.Sequence;
-import santa.simulator.phylogeny.Phylogeny;
-import santa.simulator.population.PopulationGrowth;
-import santa.simulator.population.Population;
-import santa.simulator.samplers.SamplingSchedule;
-import santa.simulator.selectors.Selector;
+import santa.simulator.compartments.Compartment;
+import santa.simulator.compartments.Compartments;
 
 /**
  * @author Andrew Rambaut
@@ -20,67 +14,67 @@
  */
 public class Simulation {
 
-    private final int populationSize;
-    private final InoculumType inoculumType;
-    private final GenePool genePool;
-    private final List<SimulationEpoch> epochs;
-    private final Selector selector;
-    private final SamplingSchedule samplingSchedule;
-
-    private final Population population;
-
-	public enum InoculumType {
-		NONE,
-		CONSENSUS,
-		RANDOM,
-		ALL
-	};
-	
-    //Default constructor
-    public Simulation (
-            int populationSize,
-            Selector selector,
-            PopulationGrowth growth,
-            InoculumType inoculumType,
-            GenePool genePool,
-            List<SimulationEpoch> epochs,
-            SamplingSchedule samplingSchedule) {
-
-        this.populationSize = populationSize;
-        this.inoculumType = inoculumType;
-        this.epochs = epochs;
-        this.samplingSchedule = samplingSchedule;
-        this.genePool = genePool;
-        this.selector = selector;
-
-        population = new Population(genePool, selector, growth, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null);
+    private List<SimulationEpoch> epochs;
+    private Compartments compartments;
+    private static Logger memlogger = Simulator.memlogger;
+    
+    public Simulation(Compartments compartments) {
+        this.compartments = compartments;
+        
+        // split CompartmentEpochs so that they have the same time slices
+        this.epochs = new ArrayList<>();
+        int compartmentEpochIndex = 0;
+        boolean cont = true;
+        
+         while (cont) {
+            int minGenerations = Integer.MAX_VALUE;
+            ArrayList<CompartmentEpoch> compartmentEpochs = new ArrayList();
+            
+            for (Compartment compartment: compartments) {
+                CompartmentEpoch currentCompartmentEpoch = compartment.getEpochs().get(compartmentEpochIndex);
+                compartmentEpochs.add(currentCompartmentEpoch);
+                
+                if (minGenerations > currentCompartmentEpoch.getGenerationCount()) {
+                    minGenerations = currentCompartmentEpoch.getGenerationCount();
+                }
+            }
+            
+            for (Compartment compartment: compartments) {
+                List<CompartmentEpoch> compartmentsEpochs = compartment.getEpochs();
+                CompartmentEpoch currentCompartmentEpoch = compartmentsEpochs.get(compartmentEpochIndex);
+                
+                if (minGenerations < currentCompartmentEpoch.getGenerationCount()) {
+                    compartmentsEpochs.add(compartmentEpochIndex + 1, new CompartmentEpoch(
+                        currentCompartmentEpoch.getName(),
+                        currentCompartmentEpoch.getGenerationCount() - minGenerations,
+                        currentCompartmentEpoch.getFitnessFunction(),
+                        currentCompartmentEpoch.getMutator(),
+                        currentCompartmentEpoch.getReplicator()));
+                }
+                
+                currentCompartmentEpoch.setGenerationCount(minGenerations);
+                
+                if (compartmentsEpochs.size() <= compartmentEpochIndex + 1)
+                    cont = false;
+            }
+            
+            this.epochs.add(new SimulationEpoch(compartmentEpochs, minGenerations));
+            
+            /* 
+             * TODO:
+             * Add check for duplicate epoch names
+             * Add check / deal with different overall epoch length
+            */
+            
+            compartmentEpochIndex++;
+        }
     }
     
     public void run(int replicate, Logger logger) {
-
-        samplingSchedule.initialize(replicate);
-
-        EventLogger.setReplicate(replicate);
-
-        logger.finer("Initializing population: " + populationSize + " viruses.");
-
-	    List<Sequence> inoculum = new ArrayList<Sequence>();
-	    if (inoculumType == InoculumType.CONSENSUS) {
-		    inoculum.add(GenomeDescription.getConsensus());
-	    } else if (inoculumType == InoculumType.ALL) {
-		    inoculum.addAll(GenomeDescription.getSequences());
-	    } else if (inoculumType == InoculumType.RANDOM) {
-		    List<Sequence> sequences = GenomeDescription.getSequences();
-		    if (sequences.size() == 1) {
-			    inoculum.add(sequences.get(0));
-		    } else {
-		        inoculum.add(sequences.get(Random.nextInt(0, sequences.size() - 1)));
-		    }
-	    } else { // NONE
-		    // do nothing
-	    }
-        population.initialize(inoculum, populationSize);
-
+        for (Compartment compartment: compartments) {
+            compartment.initalize(replicate, logger);
+        }
+        
         int generation = 1;
 
         int epochCount = 0;
@@ -89,28 +83,29 @@ public void run(int replicate, Logger logger) {
             EventLogger.setEpoch(epochCount);
 
             generation = epoch.run(this, logger, generation);
-            if(population.getCurrentGeneration().size() == 0) {
+            
+            boolean allDead = true;
+            
+            for (Compartment compartment: compartments) {
+                if (!compartment.getPopulation().getCurrentGeneration().isEmpty()) {
+                    allDead = false;
+                    break;
+                }
+            }
+        
+            if (allDead) {
             	System.err.println("Population crashed after "+generation+" generations.");
             	return;
             }
             epochCount++;
         }
-        samplingSchedule.cleanUp();
-    }
-
-    public GenePool getGenePool() {
-        return genePool;
-    }
-
-    public Population getPopulation() {
-        return population;
-    }
-
-    public int getPopulationSize() {
-        return populationSize;
+        
+        for (Compartment compartment: compartments) {
+            compartment.cleanup(replicate, logger);
+        }
     }
-
-    public SamplingSchedule getSamplingSchedule() {
-        return samplingSchedule;
+   
+    public Compartments getCompartments() {
+        return compartments;
     }
 }
diff --git a/src/santa/simulator/SimulationEpoch.java b/src/santa/simulator/SimulationEpoch.java
index 6c2699d..b04e574 100644
--- a/src/santa/simulator/SimulationEpoch.java
+++ b/src/santa/simulator/SimulationEpoch.java
@@ -1,116 +1,74 @@
-/*
- * Created on Mar 12, 2007
- *
- * To change the template for this generated file go to
- * Window>Preferences>Java>Code Generation>Code and Comments
- */
 package santa.simulator;
 
-import santa.simulator.fitness.FitnessFunction;
-import santa.simulator.genomes.GenePool;
-import santa.simulator.mutators.Mutator;
-import santa.simulator.population.Population;
-import santa.simulator.replicators.Replicator;
-import santa.simulator.samplers.SamplingSchedule;
-
+import java.util.ArrayList;
 import java.util.logging.Logger;
-
 import static santa.simulator.Simulator.readableByteCount;
 import static santa.simulator.Simulator.usedMemory;
+import santa.simulator.compartments.Compartment;
+import santa.simulator.compartments.CompartmentEpoch;
+import santa.simulator.compartments.Compartments;
+import java.util.List;
 
+/**
+ *
+ * @author Andrew Rambaut
+ */
 public class SimulationEpoch {
-    private String name;
     private int generationCount;
-    private FitnessFunction fitnessFunction;
-    private Mutator mutator;
-    private Replicator replicator;
-	private static Logger memlogger = Simulator.memlogger;
-
-    public SimulationEpoch(String name, int generationCount,
-            FitnessFunction fitnessFunction, Mutator mutator,
-            Replicator replicator) {
-        this.name = name;
+    private List<CompartmentEpoch> compartmentEpochs;
+    private String name;
+    private static Logger memlogger = Simulator.memlogger;
+   
+    public SimulationEpoch(List<CompartmentEpoch> epochs, int generationCount) {
+        this.compartmentEpochs = epochs;
         this.generationCount = generationCount;
-        this.fitnessFunction = fitnessFunction;
-        this.mutator = mutator;
-        this.replicator = replicator;
+        
+        this.name = null;
+        
+        for (CompartmentEpoch epoch: compartmentEpochs) {
+            if (name == null) {
+                epoch.getName();
+            } else {
+                this.name += ", " + epoch.getName();
+            }
+            
+        }
     }
-
+    
     public int run(Simulation simulation, Logger logger, int startGeneration) {
-        System.err.println("Starting epoch: " + (name != null ? name : "(unnamed)"));
-
-        Population population = simulation.getPopulation();
-        GenePool genePool = simulation.getGenePool();
-        SamplingSchedule samplingSchedule = simulation.getSamplingSchedule();
+        Compartments compartments = simulation.getCompartments();
 
         final int endGeneration = startGeneration + generationCount;
 
-		memlogger.fine("@start of Epoch Memory used = " + readableByteCount(usedMemory()));
+        System.err.println("Starting epochs: " + name);
+                
+        memlogger.fine("@start of Epoch Memory used = " + readableByteCount(usedMemory()));
 
         for (int generation = startGeneration; generation < endGeneration; ++generation) {
             EventLogger.setEpoch(generation);
-
-            fitnessFunction.updateGeneration(generation, population);
-
-            if (generation == startGeneration) {
-                // adapt to this epoch, and the new generation
-                population.updateAllFitnesses(fitnessFunction);
-                
-                System.err.println("Initial population:  fitness = " + population.getMeanFitness() +
-                        ", distance = " + population.getMeanDistance() +
-                        ", max freq = " + population.getMaxFrequency() +
-                        ", genepool size = " + genePool.getUniqueGenomeCount() +
-                        " (" + genePool.getUnusedGenomeCount() + " available)");                
+            
+            int i = 0;
+            int totalPopulation = 0;
+            for (Compartment compartment: compartments) {
+                totalPopulation += compartmentEpochs.get(i++).step(compartment, logger, startGeneration, generation);
             }
-
-            population.selectNextGeneration(generation, replicator, mutator, fitnessFunction);
-            if(population.getCurrentGeneration().size() == 0) {
+            
+            if (totalPopulation == 0) {
             	return generation;
             }
             
+            if (compartments.getNumCompartments() > 1)
+                compartments.genomeTransfer(generation, compartmentEpochs);
+                
             if (generation % 100 == 0) {
-                if (population.getPhylogeny() != null)
-                    population.getPhylogeny().pruneDeadLineages();
-
-				memlogger.finest("Generation "+ generation +
-							   " used memory: " + readableByteCount(usedMemory()));
-
-                System.err.print("Generation " + generation + ":  fitness = " + population.getMeanFitness() +
-                        ", distance = " + population.getMeanDistance() +
-                        ", max freq = " + population.getMaxFrequency() +
-                        ", genepool size = " + genePool.getUniqueGenomeCount() +
-                        " (" + genePool.getUnusedGenomeCount() + " available)");
-                if (population.getPhylogeny() != null) {
-                    population.getPhylogeny().pruneDeadLineages();
-                    System.err.println(", phylogeny size = " + population.getPhylogeny().getSize() +
-                        " (used = " + population.getPhylogeny().getLineageCount()+ ")" +
-                        ", tmrca = " + population.getPhylogeny().getMRCA().getGeneration() );
-                } else
-                    System.err.println();
-            } else {
-            	logger.finest("Generation " + generation + ":  fitness = " + population.getMeanFitness() +
-            			", distance = " + population.getMeanDistance() +
-            			", max freq = " + population.getMaxFrequency() +
-            			", genepool size= " + genePool.getUniqueGenomeCount() +
-            			"(" + genePool.getUnusedGenomeCount() + " available)");                
+                memlogger.finest("Generation "+ generation + " used memory: " + readableByteCount(usedMemory()));
             }
-
-            samplingSchedule.doSampling(generation, population);
         }
 
         return endGeneration;
     }
-
-    public FitnessFunction getFitnessFunction() {
-        return fitnessFunction;
-    }
-
-    public Mutator getMutator() {
-        return mutator;
-    }
-
-    public Replicator getReplicator() {
-        return replicator;
+    
+    public String getName() {
+        return name;
     }
-
 }
diff --git a/src/santa/simulator/SimulatorMain.java b/src/santa/simulator/SimulatorMain.java
index ee6db7b..ea14e20 100644
--- a/src/santa/simulator/SimulatorMain.java
+++ b/src/santa/simulator/SimulatorMain.java
@@ -21,7 +21,7 @@ public static void main(String[] args) {
 		Simulator simulator;
 
         if (args.length > 0) {
-			simulator = simulatorFactory(args);
+		simulator = simulatorFactory(args);
 
 	        Logger.getLogger("santa.simulator").addHandler(new ConsoleHandler());
 
diff --git a/src/santa/simulator/SimulatorParser.java b/src/santa/simulator/SimulatorParser.java
index b2d39b9..a6947bc 100644
--- a/src/santa/simulator/SimulatorParser.java
+++ b/src/santa/simulator/SimulatorParser.java
@@ -1,6 +1,7 @@
 
 package santa.simulator;
 
+import santa.simulator.compartments.CompartmentEpoch;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.io.PrintWriter;
@@ -17,6 +18,13 @@
 import static java.nio.file.Paths.get;
 
 import org.jdom2.Element;
+import santa.simulator.compartments.Compartment;
+import santa.simulator.compartments.Compartments;
+import santa.simulator.compartments.DoubleProb;
+import santa.simulator.compartments.FitnessProb;
+import santa.simulator.compartments.MatrixTransfer;
+import santa.simulator.compartments.TimedTransfer;
+import santa.simulator.compartments.TransferProb;
 
 import santa.simulator.fitness.AgeDependentFitnessFactor;
 import santa.simulator.fitness.BetaDistributedPurifyingFitnessModel;
@@ -24,6 +32,7 @@
 import santa.simulator.fitness.FitnessFactor;
 import santa.simulator.fitness.FitnessFunction;
 import santa.simulator.fitness.FrequencyDependentFitnessFactor;
+import santa.simulator.fitness.NoFitnessFactor;
 import santa.simulator.fitness.PopulationSizeDependentFitnessFactor;
 import santa.simulator.fitness.PurifyingFitnessFactor;
 import santa.simulator.fitness.PurifyingFitnessModel;
@@ -56,8 +65,8 @@
 import santa.simulator.samplers.StatisticsSampler;
 import santa.simulator.samplers.TreeSampler;
 import santa.simulator.samplers.GenomeDescriptionSampler;
-import santa.simulator.IndelModel;
 import santa.simulator.selectors.BinarySearchSelector;
+import santa.simulator.selectors.ClonalExpansionSelector;
 import santa.simulator.selectors.DynamicSelector;
 import santa.simulator.selectors.Selector;
 
@@ -73,7 +82,18 @@ public class SimulatorParser {
 	private final static String REPLICATE_COUNT = "replicates";
 
 	private final static String SIMULATION = "simulation";
-
+        
+        private final static String COMPARTMENT = "compartment";
+        private final static String TRANSFER_RATES = "transferRates";
+        
+        private final static String FITNESS_TRANSFER = "transferFitness";
+        
+        private final static String TIMED_TRANSFER = "timedTransfer";
+        private final static String TO_COMPARTMENT = "toCompartment";
+        private final static String FROM_COMPARTMENT = "fromCompartment";
+        private final static String TRANSFER_GENERATION = "generation";
+        private final static String TRANSFER_AMOUNT = "amountToTransfer";
+        
 	private final static String EPOCH = "epoch";
 	private final static String NAME = "name";
 	private final static String GENERATION_COUNT = "generationCount";
@@ -83,6 +103,10 @@ public class SimulatorParser {
 	private final static String POPULATION_TYPE = "populationType";
 	private final static String STATIC_POPULATION = "staticPopulation";
 	private final static String DYNAMIC_POPULATION = "dynamicPopulation";
+        private final static String EXPONENTIAL_POPULATION = "exponentialPopulation";
+        private final static String LOGISTIC_POPULATION = "logisticPopulation";
+        private final static String MAX_POPULATION_SIZE = "maxPopulationSize";
+        
 	
 	private final static String RECOMBINATION_HOTSPOTS = "recombinationHotSpots";
 	private final static String RECOMBINATION_HOTSPOT = "recombinationHotSpot";
@@ -95,8 +119,10 @@ public class SimulatorParser {
 	private final static String INOCULUM_ALL = "all";
 
 	private final static String GROWTH_MODEL = "growthModel";
-	private final static String GROWTH_RATE = "growthRate";
+        private final static String GROWTH_RATE = "growthRate";
 	private final static String CARRYING_POPULATION = "carryingPopulation";
+        private final static String SPLIT_PROBABILITY = "split";
+        private final static String DEATH_PROBABILITY = "death";
 	
 	private final static String GENOME_DESCRIPTION = "genome";
 	private final static String GENOME_LENGTH = "length";
@@ -148,6 +174,7 @@ public class SimulatorParser {
 	private final static String EMPIRICAL_FITNESS_FUNCTION = "empiricalFitness";
 	private final static String POPULATION_SIZE_DEPENDENT_FITNESS_FUNCTION = "populationSizeDependentFitness";
 	private final static String MAX_POP_SIZE = "maxPopulationSize";
+        private final static String NO_FITNESS_FUNCTION = "noFitness";
 
 	private final static String MUTATOR = "mutator";
 	private final static String REPLICATOR = "replicator";
@@ -198,7 +225,7 @@ public class SimulatorParser {
 	/*
 	 * Object Cache methods
 	 */
-	private Map<String, Object> objectIdMap = new HashMap<String, Object>();
+	private Map<String, Object> objectIdMap = new HashMap<>();
 
     private Object lookupObjectById(String id, Class<? extends Object> expectedType) throws ParseException {
 		
@@ -295,79 +322,203 @@ Simulator parse(Element element) throws ParseException {
 		return simulator;
 	}
 
-	//Default populationType is dynamicPopulation but in the xml file static population could be selected
-	Simulation parseSimulation(Element element) throws ParseException {
-
-		Simulation.InoculumType inoculumType = Simulation.InoculumType.NONE;
-
-		int populationSize = -1;
-
-		boolean genomeDescription = false;
-		for (Object o : element.getChildren()) {
-			Element e = (Element)o;
-			if (e.getName().equals(GENOME_DESCRIPTION)) {
-				parseGenomeDescription(e);
-				genomeDescription = true;
-			}
-		}
-
-		if (!genomeDescription) {
-			throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + GENOME_DESCRIPTION + "> is missing");
-		}
-
-		for (Object o : element.getChildren()) {
-			Element e = (Element)o;
-			if (e.getName().equals(POPULATION)) {
-
-				for (Object o1 : e.getChildren()) {
-					Element e1 = (Element)o1;
-					if (e1.getName().equals(POPULATION_SIZE)) {
-						try {
-							populationSize = parseInteger(e1, 1, Integer.MAX_VALUE);
-						} catch (ParseException pe) {
-							throw new ParseException("Error parsing <" + POPULATION + "> element: " + pe.getMessage());
-						}
-					} else if (e1.getName().equals(INOCULUM)) {
-						String v = e1.getTextNormalize();
-						if (v.equals(INOCULUM_NONE)) {
-							inoculumType = Simulation.InoculumType.NONE;
-						} else if (v.equals(INOCULUM_CONSENSUS)) {
-							inoculumType = Simulation.InoculumType.CONSENSUS;
-						} else if (v.equals(INOCULUM_RANDOM)) {
-							inoculumType = Simulation.InoculumType.RANDOM;
-						} else if (v.equals(INOCULUM_ALL)) {
-							inoculumType = Simulation.InoculumType.ALL;
-						} else {
-							// do nothing
-						}
-					} else {
-						throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + e.getName() + "> is unrecognized");
-					}
-				}
-			} else if (!e.getName().equals(GENOME_DESCRIPTION) &&
-					!e.getName().equals(GENE_POOL) &&
-					!e.getName().equals(FITNESS_FUNCTION) &&
-					!e.getName().equals(MUTATOR) &&
-					!e.getName().equals(REPLICATOR) &&
-					!e.getName().equals(SAMPLING_SCHEDULE) &&
-					!e.getName().equals(EVENT_LOGGER) &&
-					!e.getName().equals(EPOCH) &&
-					!e.getName().equals(POPULATION_TYPE) &&
+    Simulation parseSimulation(Element element) throws ParseException {
+        Compartments compartments = null;
+        ArrayList<Compartment> compartmentList = new ArrayList<>();
+        
+        boolean genomeDescription = false;
+        for (Object o : element.getChildren()) {
+            Element e1 = (Element)o;
+            if (e1.getName().equals(GENOME_DESCRIPTION)) {
+                parseGenomeDescription(e1);
+                genomeDescription = true;
+            }
+        }
+        
+        if (!genomeDescription) {
+            throw new ParseException("Error parsing <" + element.getName() + "> element: <" + GENOME_DESCRIPTION + "> is missing");
+        }
+        
+        ArrayList<TransferProb> transferRates = new ArrayList<>();
+        ArrayList<TimedTransfer.TransferEvent> transferEvents = new ArrayList<>();
+        
+        Element e = element.getChildren().get(0);
+        switch (e.getName()) {
+            case TRANSFER_RATES:
+            case TIMED_TRANSFER:
+            case FITNESS_TRANSFER:
+                for (Object o: element.getChildren()) {
+                    Element e2 = (Element)o;
+                    switch (e2.getName()) {
+                        case COMPARTMENT:
+                            compartmentList.add(parseCompartment(e2));
+                            break;
+                        case TRANSFER_RATES:
+                            double[] parsedRates = parseNumberList(e2);
+                            
+                            for (int i = 0; i < parsedRates.length; i++) {
+                                transferRates.add(new DoubleProb(parsedRates[i]));
+                            }
+                            
+                            break;
+                        case FITNESS_TRANSFER:
+                            for (Object o3: e2.getChildren()) {
+                                Element e3 = (Element)o3;
+                                
+                                if (e3.getName().equals(FITNESS_FUNCTION)) {
+                                    FitnessFunction fitness = parseFitnessFunction(e3);
+                                    
+                                    transferRates.add(new FitnessProb(fitness));
+                                } else {
+                                    throw new ParseException("Error parsing <" + FITNESS_TRANSFER + "> element: <" + e3.getName() + "> is unrecognized");
+                                }                                
+                            }
+                            break;
+                        case TIMED_TRANSFER:
+                            transferEvents.add(parseTransferEvent(e2));
+                            break;
+                        case GENOME_DESCRIPTION:
+                            break;
+                        default:
+                            throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + e2.getName() + "> is unrecognized");
+                    }
+                }
+            
+                if (transferRates.isEmpty() && transferEvents.isEmpty()) {
+                    throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + TRANSFER_RATES + "> is missing");
+                }
+            
+                if (compartmentList.isEmpty()) {
+                    throw new ParseException("Error parsing <" + SIMULATION + "> no <" + COMPARTMENT + "> found");
+                }
+            
+                if (transferRates.isEmpty() && transferRates.size() != compartmentList.size() * compartmentList.size()) {
+                    throw new ParseException(
+                        "Error parsing <" +
+                            SIMULATION +
+                            "> element: <" + 
+                            TRANSFER_RATES + 
+                            "> should be size (" + 
+                            compartmentList.size() * compartmentList.size() + 
+                            "), but was (" +
+                            transferRates.size() +
+                            ") instead"
+                    );
+                }
+                    
+                break;                
+            default:
+                transferRates.add(new DoubleProb(1));
+                
+                compartmentList.add(parseCompartment(element));                
+                break;
+        }
+        
+        if (!transferEvents.isEmpty()) {
+            ArrayList<String> compartmentNames = new ArrayList<>();
+            
+            for (Compartment compartment: compartmentList) {
+                compartmentNames.add(compartment.getName());
+            }
+            
+            for (TimedTransfer.TransferEvent event: transferEvents) {
+                if (!event.findCompartmentIndices(compartmentNames)) {
+                    throw new ParseException("Compartment not found for timedTransfer");
+                }
+            }
+            
+            compartments = new Compartments(compartmentList, new TimedTransfer(transferEvents));
+        } else {
+            compartments = new Compartments(compartmentList, new MatrixTransfer(transferRates, compartmentList.size()));
+        }
+        
+        return new Simulation(compartments);
+    }
+    
+    //Default populationType is dynamicPopulation but in the xml file static population could be selected
+    Compartment parseCompartment(Element element) throws ParseException {
+        Compartment.InoculumType inoculumType = Compartment.InoculumType.NONE;
+        int populationSize = -1;
+        int maxPopulationSize = -1;
+        double growthRate = -1;
+
+	for (Object o : element.getChildren()) {
+            Element e = (Element)o;
+            if (e.getName().equals(POPULATION)) {
+                for (Object o1 : e.getChildren()) {
+                    Element e1 = (Element)o1;
+                    switch (e1.getName()) {
+                        case POPULATION_SIZE:
+                            try {
+                                populationSize = parseInteger(e1, 0, Integer.MAX_VALUE);
+                            } catch (ParseException pe) {
+                                throw new ParseException("Error parsing <" + POPULATION + "> element: " + pe.getMessage());
+                            }
+                            break;
+                        case MAX_POPULATION_SIZE:
+                            try {
+                                maxPopulationSize = parseInteger(e1, 1, Integer.MAX_VALUE);
+                            } catch (ParseException pe) {
+                                throw new ParseException("Error parsing <" + POPULATION + "> element: " + pe.getMessage());
+                            }
+                            break;
+                        case GROWTH_RATE:
+                            try {
+                                growthRate = parseDouble(e1, 0, Double.MAX_VALUE);
+                            } catch (ParseException pe) {
+                                throw new ParseException("Error parsing <" + POPULATION + "> element: " + pe.getMessage());
+                            }
+                            break;
+                        case INOCULUM:
+                            String v = e1.getTextNormalize();
+                            switch (v) {
+                                case INOCULUM_NONE:
+                                    inoculumType = Compartment.InoculumType.NONE;
+                                    break;
+                                case INOCULUM_CONSENSUS:
+                                    inoculumType = Compartment.InoculumType.CONSENSUS;
+                                    break;
+                                case INOCULUM_RANDOM:
+                                    inoculumType = Compartment.InoculumType.RANDOM;
+                                    break;
+                                case INOCULUM_ALL:
+                                    inoculumType = Compartment.InoculumType.ALL;
+                                    break;
+                                    // do nothing
+                                default:
+                                    break;
+                            }
+                            break;
+                        default:
+                            throw new ParseException("Error parsing <" + e.getName() + "> element: <" + e1.getName() + "> is unrecognized");
+                    }
+                }
+            } else if (	!e.getName().equals(GENE_POOL) &&
+                    !e.getName().equals(FITNESS_FUNCTION) &&
+                    !e.getName().equals(MUTATOR) &&
+                    !e.getName().equals(REPLICATOR) &&
+                    !e.getName().equals(SAMPLING_SCHEDULE) &&
+                    !e.getName().equals(EVENT_LOGGER) &&
+                    !e.getName().equals(EPOCH) &&
+                    !e.getName().equals(POPULATION_TYPE) &&
                     !e.getName().equals(GROWTH_MODEL) &&
-					!e.getName().equals(RECOMBINATION_HOTSPOTS)) {
-				throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + e.getName() + "> is unrecognized");
-			}
-		}
+                    !e.getName().equals(RECOMBINATION_HOTSPOTS) &&
+                    !e.getName().equals(NAME) &&
+                    !e.getName().equals(GENOME_DESCRIPTION)) {
+                throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized");
+            }
+        }
 		
 		
 		if (populationSize == -1) {
-			throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + POPULATION_SIZE + "> is missing");
+			throw new ParseException("Error parsing <" + element.getName() + "> element: <" + POPULATION_SIZE + "> is missing");
 		}
 
 		if (!GenomeDescription.isSet()) {
-			throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + GENOME_DESCRIPTION + "> is missing");
+			throw new ParseException("Error parsing <" + element.getName() + "> element: <" + GENOME_DESCRIPTION + "> is missing");
 		}
 		
+                String compartmentName = "";
 		SamplingSchedule samplingSchedule = null;
 		GenePool genePool = null;
 
@@ -376,61 +527,76 @@ Simulation parseSimulation(Element element) throws ParseException {
 		Replicator defaultReplicator = null;
 		
 		String populationType = null;
-        DynamicSelector dynamicSelector = null;
+         Selector dynamicSelector = null;
 
-		List<RecombinationHotSpot> recombinationHotSpots = new ArrayList<RecombinationHotSpot>();		
+		List<RecombinationHotSpot> recombinationHotSpots = new ArrayList<>();		
 		
 		for (Object o : element.getChildren()) {
 			Element e = (Element)o;
 			String name = e.getName();
-			if (name.equals(GENE_POOL)) {
-				genePool = parseGenePool(e);
-			} else if (name.equals(SAMPLING_SCHEDULE)) {
-				samplingSchedule = parseSamplingSchedule(e);
-			} else if (name.equals(EVENT_LOGGER)) {
-				parseEventLogger(e);
-			} else if (name.equals(FITNESS_FUNCTION)) {
-				defaultFitnessFunction = parseFitnessFunction(e);
-			} else if (name.equals(MUTATOR)) {
-				defaultMutator = parseMutator(e);
-			} else if (name.equals(RECOMBINATION_HOTSPOTS)){
-				recombinationHotSpots = parseRecombinationHotSpots(e);
-				GenomeDescription.setHotSpots(recombinationHotSpots);
-			} else if (name.equals(POPULATION_TYPE)){
-				populationType = (String) e.getTextNormalize();
-			} else if (name.equals(REPLICATOR)) {
-				defaultReplicator = parseReplicator(e);
-			} else if (name.equals(GROWTH_MODEL)) {
-                dynamicSelector = parseGrowthModel(e);
-            }
+                    switch (name) {
+                        case NAME:
+                            compartmentName = (String)e.getTextNormalize();
+                            break;
+                        case GENE_POOL:
+                            genePool = parseGenePool(e);
+                            break;
+                        case SAMPLING_SCHEDULE:
+                            samplingSchedule = parseSamplingSchedule(e);
+                            break;
+                        case EVENT_LOGGER:
+                            parseEventLogger(e);
+                            break;
+                        case FITNESS_FUNCTION:
+                            defaultFitnessFunction = parseFitnessFunction(e);
+                            break;
+                        case MUTATOR:
+                            defaultMutator = parseMutator(e);
+                            break;
+                        case RECOMBINATION_HOTSPOTS:
+                            recombinationHotSpots = parseRecombinationHotSpots(e);
+                            GenomeDescription.setHotSpots(recombinationHotSpots);
+                            break;
+                        case POPULATION_TYPE:
+                            populationType = (String)e.getTextNormalize();
+                            break;
+                        case REPLICATOR:
+                            defaultReplicator = parseReplicator(e);
+                            break;
+                        case GROWTH_MODEL:
+                            dynamicSelector = parseGrowthModel(e);
+                            break;
+                        default:
+                            break;
+                    }
 		}
 
 		if (samplingSchedule == null)
-			throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + SAMPLING_SCHEDULE + "> is missing");
+			throw new ParseException("Error parsing <" + element.getName() + "> element: <" + SAMPLING_SCHEDULE + "> is missing");
 
 		if (genePool == null) {
 			genePool = new SimpleGenePool();
 		}
 
 		if (defaultFitnessFunction == null)
-			throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + FITNESS_FUNCTION + "> is missing");
+			throw new ParseException("Error parsing <" + element.getName() + "> element: <" + FITNESS_FUNCTION + "> is missing");
 
 		if (defaultMutator == null)
-			throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + MUTATOR + "> is missing");
+			throw new ParseException("Error parsing <" + element.getName() + "> element: <" + MUTATOR + "> is missing");
 
 		if (defaultReplicator == null)
-			throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + REPLICATOR + "> is missing");
+			throw new ParseException("Error parsing <" + element.getName() + "> element: <" + REPLICATOR + "> is missing");
 		
 		if (populationType == null) {
 			populationType = STATIC_POPULATION;
         }
 
-		List<SimulationEpoch> epochs = new ArrayList<SimulationEpoch>();
+		List<CompartmentEpoch> epochs = new ArrayList<>();
 		
 		for (Object o : element.getChildren()) {
 			Element e = (Element)o;
 			if (e.getName().equals(EPOCH)) {
-				SimulationEpoch epoch = parseSimulationEpoch(e,
+				CompartmentEpoch epoch = parseSimulationEpoch(e,
 						defaultFitnessFunction, defaultMutator, defaultReplicator);
 
 				epochs.add(epoch);
@@ -438,51 +604,113 @@ Simulation parseSimulation(Element element) throws ParseException {
 		}
 
 		if (epochs.isEmpty())
-			throw new ParseException("Error parsing <" + SIMULATION + "> element: <" + EPOCH + "> is missing");
-		
+			throw new ParseException("Error parsing <" + element.getName() + "> element: <" + EPOCH + "> is missing");
 		
-		if (populationType.equals(STATIC_POPULATION)) {
-			Selector selector = new BinarySearchSelector();
-			PopulationGrowth growth = new StaticPopulationGrowth(populationSize);
-			return new  Simulation(populationSize, selector, growth, inoculumType, genePool, epochs, samplingSchedule);
-		} else if (populationType.equals(DYNAMIC_POPULATION)) {
-			PopulationGrowth growth = new DynamicPopulationGrowth();
-			Selector selector = null;
+            Selector selector;
+            PopulationGrowth growth;
+                
+            switch (populationType) {
+                case STATIC_POPULATION:
+                    selector = new BinarySearchSelector();
+                    growth = new StaticPopulationGrowth(populationSize);
+                    return new  Compartment(compartmentName, populationSize, selector, growth, inoculumType, genePool, epochs, samplingSchedule);
+                case DYNAMIC_POPULATION:
+                    growth = new DynamicPopulationGrowth();
+                    selector = null;
+                    
 		    if (dynamicSelector == null) {
 		    	selector = new DynamicSelector();
 		    } else {
 		    	selector = dynamicSelector;
 		    }
-		    	
-		    return new Simulation(populationSize, selector, growth, inoculumType, genePool, epochs, samplingSchedule);
-		}
-		else throw new ParseException("unrecognized population type. should be either staticPopulation or dynamicPopulation.");
-		
+                    
+                    return new Compartment(compartmentName, populationSize, selector, growth, inoculumType, genePool, epochs, samplingSchedule);
+                default:
+                    throw new ParseException("unrecognized population type. should be either staticPopulation or dynamicPopulation.");
+            }		
 	}
 
-	DynamicSelector parseGrowthModel(Element element) throws ParseException {
+	Selector parseGrowthModel(Element element) throws ParseException {
 	    double growthRate = -1;
 	    double carryingPopulation = -1;
+            double split = -1;
+            double death = -1;
         for (Object o : element.getChildren()) {
             Element e = (Element)o;
-            if (e.getName().equals(GROWTH_RATE)) {
-                growthRate = Double.parseDouble(e.getTextNormalize());
-            } else if (e.getName().equals(CARRYING_POPULATION)) {
-                carryingPopulation = Double.parseDouble(e.getTextNormalize());
-            } else {
-                throw new ParseException("Error parsing <" + GROWTH_MODEL + "> element: unknown XML element within " + GROWTH_MODEL);
-            }
+                switch (e.getName()) {
+                    case GROWTH_RATE:
+                        growthRate = Double.parseDouble(e.getTextNormalize());
+                        break;
+                    case CARRYING_POPULATION:
+                        carryingPopulation = Double.parseDouble(e.getTextNormalize());
+                        break;
+                    case SPLIT_PROBABILITY:
+                        split = Double.parseDouble(e.getTextNormalize());
+                        break;
+                    case DEATH_PROBABILITY:
+                        death = Double.parseDouble(e.getTextNormalize());
+                        break;
+                    default:
+                        throw new ParseException("Error parsing <" + GROWTH_MODEL + "> element: unknown XML element within " + GROWTH_MODEL);
+                }
         }
 
         if (growthRate != -1 && carryingPopulation != -1) {
             return new DynamicSelector(growthRate, carryingPopulation);
+        } else if (split != -1 && death != -1) {
+            return new ClonalExpansionSelector(split, death);
         } else {
             return null;
         }
 
+    }
+        
+    TimedTransfer.TransferEvent parseTransferEvent(Element element) throws ParseException {
+        String toCompartment = null;
+        String fromCompartment = null;
+        int generation = -1;
+        int amountToTransfer = -1;
+        
+        for (Object o : element.getChildren()) {
+            Element e = (Element)o;
+            switch (e.getName()){
+                case TO_COMPARTMENT:
+                    toCompartment = e.getTextNormalize();
+                    break;
+                case FROM_COMPARTMENT:
+                    fromCompartment = e.getTextNormalize();
+                    break;
+                case TRANSFER_GENERATION:
+                    generation = Integer.parseInt(e.getTextNormalize());
+                    break;
+                case TRANSFER_AMOUNT:
+                    amountToTransfer = Integer.parseInt(e.getTextNormalize());
+                    break;
+                default:
+                    throw new ParseException("Error parsing <" + TIMED_TRANSFER + "> element: unknown XML element within " + TIMED_TRANSFER);
+            }                   
+        }
+        
+        if (toCompartment == null) {
+            throw new ParseException("Error parsing <" + TIMED_TRANSFER + "> element: " + TO_COMPARTMENT + " was not found");
+        }
+        
+        if (fromCompartment == null) {
+            throw new ParseException("Error parsing <" + TIMED_TRANSFER + "> element: " + FROM_COMPARTMENT + " was not found");
+        }
+        
+        if (generation < 0) {
+            throw new ParseException("Error parsing <" + TIMED_TRANSFER + "> element: " + TRANSFER_GENERATION + " is negative or was not found");
+        }
+        
+        if (amountToTransfer < 0) {
+            throw new ParseException("Error parsing <" + TIMED_TRANSFER + "> element: " + TRANSFER_AMOUNT + " is negative or was not found");
+        }
+        
+        return new TimedTransfer.TransferEvent(toCompartment, fromCompartment, generation, amountToTransfer);
     }
 	
-	SimulationEpoch parseSimulationEpoch(Element element,
+	CompartmentEpoch parseSimulationEpoch(Element element,
 	                                     FitnessFunction fitnessFunction, Mutator mutator,
 	                                     Replicator replicator) throws ParseException {
 
@@ -512,50 +740,60 @@ SimulationEpoch parseSimulationEpoch(Element element,
 
 		for (Object o : element.getChildren()) {
 			Element e = (Element)o;
-			if (e.getName().equals(FITNESS_FUNCTION)) {
-				fitnessFunction = parseFitnessFunction(e);
-			} else if (e.getName().equals(MUTATOR)) {
-				mutator = parseMutator(e);
-			} else if (e.getName().equals(REPLICATOR)) {
-				replicator = parseReplicator(e);
-			}
+                    switch (e.getName()) {
+                        case FITNESS_FUNCTION:
+                            fitnessFunction = parseFitnessFunction(e);
+                            break;
+                        case MUTATOR:
+                            mutator = parseMutator(e);
+                            break;
+                        case REPLICATOR:
+                            replicator = parseReplicator(e);
+                            break;
+                        default:
+                            break;
+                    }
 		}
 
-		return new SimulationEpoch(name, generationCount, fitnessFunction, mutator, replicator);
+		return new CompartmentEpoch(name, generationCount, fitnessFunction, mutator, replicator);
 	}
 
 	private void parseGenomeDescription(Element element) throws ParseException {
 
 		int genomeLength = -1;
-		List<Feature> features = new ArrayList<Feature>();
+		List<Feature> features = new ArrayList<>();
 		List<Sequence> sequences = null;
 
 		for (Object o : element.getChildren()) {
 			Element e = (Element)o;
-			if (e.getName().equals(GENOME_LENGTH)) {
-				try {
-					genomeLength = parseInteger(e, 1, Integer.MAX_VALUE);
-				} catch (ParseException pe) {
-					throw new ParseException("Error parsing <" + GENOME_DESCRIPTION + "> element: " + pe.getMessage());
-				}
-			} else if (e.getName().equals(FEATURE)) {
-                features.add(parseFeature(e));
-			} else if (e.getName().equals(SEQUENCES)) {
-				if (e.getAttributeValue(FILENAME) != null) {
-					try {
-						// quick and dirty one-liner to read in a text file.
-						// http://jdevelopment.nl/java-7-oneliner-read-file-string/
-						String text = new String(readAllBytes(get(e.getAttributeValue(FILENAME))));
-						sequences = parseAlignment(text);
-					} catch (IOException eio) {
-						throw new ParseException("Error parsing <" + SEQUENCES + "> file attribute: Cannot open file " + eio.getMessage());
-					}
-				} else {
-					sequences = parseAlignment(e.getTextTrim());
-				}
-			} else  {
-				throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized");
-			}
+                    switch (e.getName()) {
+                        case GENOME_LENGTH:
+                            try {
+                                genomeLength = parseInteger(e, 1, Integer.MAX_VALUE);
+                            } catch (ParseException pe) {
+                                throw new ParseException("Error parsing <" + GENOME_DESCRIPTION + "> element: " + pe.getMessage());
+                            }
+                            break;
+                        case FEATURE:
+                            features.add(parseFeature(e));
+                            break;
+                        case SEQUENCES:
+                            if (e.getAttributeValue(FILENAME) != null) {
+                                try {
+                                    // quick and dirty one-liner to read in a text file.
+                                    // http://jdevelopment.nl/java-7-oneliner-read-file-string/
+                                    String text = new String(readAllBytes(get(e.getAttributeValue(FILENAME))));
+                                    sequences = parseAlignment(text);
+                                } catch (IOException eio) {
+                                    throw new ParseException("Error parsing <" + SEQUENCES + "> file attribute: Cannot open file " + eio.getMessage());
+                                }
+                            } else {
+                                sequences = parseAlignment(e.getTextTrim());
+                            }
+                            break;
+                        default:
+                            throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized");
+                    }
 		}
 
 		if (genomeLength == -1) {
@@ -570,30 +808,37 @@ private Feature parseFeature(Element element) throws ParseException {
 		String name = null;
 		Feature.Type type = Feature.Type.NUCLEOTIDE;
 		String sites = null;
-		List<String> parts = new ArrayList<String>();
+		List<String> parts = new ArrayList<>();
 
 		for (Object o : element.getChildren()) {
 			Element e = (Element) o;
 
-			if (e.getName().equals(NAME)) {
-				name = e.getTextNormalize();
-			} else if (e.getName().equals(TYPE)) {
-				if (e.getTextNormalize().equals(AMINO_ACID)) {
-					type = Feature.Type.AMINO_ACID;
-				} else if (e.getTextNormalize().equals(NUCLEOTIDE)) {
-					type = Feature.Type.NUCLEOTIDE;
-				} else {
-					String msg = String.format("Error parsing <%s> element: <%s> should be '%s' or '%s'",
-											   element.getName(), e.getName(),NUCLEOTIDE, AMINO_ACID);
-					throw new ParseException(msg);
-				}
-			} else if (e.getName().equals(COORDINATES)) {
-				sites = e.getTextNormalize();
-				parts = Arrays.asList(sites.split(","));
-			} else {
-				throw new ParseException("Error parsing <" + element.getName()
-						+ "> element: <" + e.getName() + "> is unrecognized");
-			}
+                    switch (e.getName()) {
+                        case NAME:
+                            name = e.getTextNormalize();
+                            break;
+                        case TYPE:
+                        switch (e.getTextNormalize()) {
+                            case AMINO_ACID:
+                                type = Feature.Type.AMINO_ACID;
+                                break;
+                            case NUCLEOTIDE:
+                                type = Feature.Type.NUCLEOTIDE;
+                                break;
+                            default:
+                                String msg = String.format("Error parsing <%s> element: <%s> should be '%s' or '%s'",
+                                        element.getName(), e.getName(),NUCLEOTIDE, AMINO_ACID);
+                                throw new ParseException(msg);
+                        }
+                            break;
+                        case COORDINATES:
+                            sites = e.getTextNormalize();
+                            parts = Arrays.asList(sites.split(","));
+                            break;
+                        default:
+                            throw new ParseException("Error parsing <" + element.getName()
+                                    + "> element: <" + e.getName() + "> is unrecognized");
+                    }
 		}
 
 		Feature feature = new Feature(name, type);
@@ -646,7 +891,7 @@ private RecombinationHotSpot parseRecombinationHotSpot(Element element) throws P
 	}
 	
 	private List<RecombinationHotSpot> parseRecombinationHotSpots(Element element) throws ParseException{
-		List<RecombinationHotSpot> recombinationHotSpots = new ArrayList<RecombinationHotSpot>();		
+		List<RecombinationHotSpot> recombinationHotSpots = new ArrayList<>();		
 		for (Object o : element.getChildren()) {
 			Element e = (Element) o;
 			RecombinationHotSpot segment = null;			
@@ -659,30 +904,41 @@ private List<RecombinationHotSpot> parseRecombinationHotSpots(Element element) t
 	}
 	
 	private FitnessFunction parseFitnessFunction(Element element) throws ParseException {
-		List<FitnessFactor> components = new ArrayList<FitnessFactor>();
+		List<FitnessFactor> components = new ArrayList<>();
 
 		for (Object o : element.getChildren()) {
 			Element e = (Element) o;
 			FitnessFactor factor = null;
 
-			if (e.getName().equals(NEUTRAL_MODEL_FITNESS_FUNCTION)) {
-				// don't need to add a factor to the product
-			} else if (e.getName().equals(PURIFYING_FITNESS_FUNCTION)) {
-				factor = parsePurifyingFitnessFunction(e);
-			} else if (e.getName().equals(EMPIRICAL_FITNESS_FUNCTION)) {
-				factor = parseEmpiricalFitnessFunction(e);
-			} else if (e.getName().equals(FREQUENCY_DEPENDENT_FITNESS_FUNCTION)) {
-				factor = parseFrequencyDependentFitnessFunction(e);
-			} else if (e.getName().equals(AGE_DEPENDENT_FITNESS_FUNCTION)) {
-				factor = parseAgeDependentFitnessFunction(e);
-			} else if (e.getName().equals(EXPOSURE_DEPENDENT_FITNESS_FUNCTION)) {
-				factor = parseExposureDependentFitnessFunction(e);
-			} else if (e.getName().equals(POPULATION_SIZE_DEPENDENT_FITNESS_FUNCTION)) {
-				factor = parsePopulationSizeDependentFitnessFunction(e);
-			} else {
-				throw new ParseException("Error parsing <" + element.getName()
-						+ "> element: <" + e.getName() + "> is unrecognized");
-			}
+                    switch (e.getName()) {
+                    // don't need to add a factor to the product
+                        case NEUTRAL_MODEL_FITNESS_FUNCTION:
+                            break;
+                        case PURIFYING_FITNESS_FUNCTION:
+                            factor = parsePurifyingFitnessFunction(e);
+                            break;
+                        case EMPIRICAL_FITNESS_FUNCTION:
+                            factor = parseEmpiricalFitnessFunction(e);
+                            break;
+                        case FREQUENCY_DEPENDENT_FITNESS_FUNCTION:
+                            factor = parseFrequencyDependentFitnessFunction(e);
+                            break;
+                        case AGE_DEPENDENT_FITNESS_FUNCTION:
+                            factor = parseAgeDependentFitnessFunction(e);
+                            break;
+                        case EXPOSURE_DEPENDENT_FITNESS_FUNCTION:
+                            factor = parseExposureDependentFitnessFunction(e);
+                            break;
+                        case POPULATION_SIZE_DEPENDENT_FITNESS_FUNCTION:
+                            factor = parsePopulationSizeDependentFitnessFunction(e);
+                            break;
+                        case NO_FITNESS_FUNCTION:
+                            factor = parseNoFitnessFunction(e);
+                            break;
+                        default:
+                            throw new ParseException("Error parsing <" + element.getName()
+                                    + "> element: <" + e.getName() + "> is unrecognized");
+                    }
 
 			if (factor != null) {
 				components.add(factor);
@@ -809,6 +1065,12 @@ private FitnessFactor parsePopulationSizeDependentFitnessFunction(Element elemen
 		return new PopulationSizeDependentFitnessFactor((int) maxPopSize, declineRate, factor.feature, factor.sites);
 	}
 
+        private FitnessFactor parseNoFitnessFunction(Element element) throws ParseException {
+            FeatureAndSites factor = parseFeatureAndSites(element);
+            
+            return new NoFitnessFactor(factor.feature, factor.sites);
+        }
+
 	/**
 	 * @param element
 	 * @return
@@ -993,9 +1255,9 @@ private FeatureAndSites parseFeatureAndSites(Element element) throws ParseExcept
             }
         }
 
-        if (sites == null || sites.size() == 0) {
+        if (sites == null || sites.isEmpty()) {
             // assume the full length of the feature
-            sites = new TreeSet<Integer>();
+            sites = new TreeSet<>();
             for (int i = 0; i < feature.getLength(); i++) {
                 sites.add(i);
             }
@@ -1017,54 +1279,55 @@ private PurifyingFitnessModel parsePurifyingFitnessModel(Element element, Featur
 		for (Object o:element.getChildren()) {
 			Element e = (Element) o;
 
-            if (e.getName().equals(BETA_DISTIBUTED)) {
-
-                // Carrasco et al (2007)  J Virology 81:12979-12984
-                double a = 1.151;
-                double b = 1.709;
-                double pLethal = 0.4;
-
-                int alphabetSize = alphabet.getStateCount();
-                int sites = factor.sites.size();
-
-                Element aChild = e.getChild("a");
-                a = Double.parseDouble(aChild.getText());
-                Element bChild = e.getChild("b");
-                b = Double.parseDouble(bChild.getText());
-                Element pChild = e.getChild("pLethal");
-                pLethal = Double.parseDouble(pChild.getText());
-
-                return new BetaDistributedPurifyingFitnessModel(a,b, pLethal, alphabetSize, sites);
-            }
-            else if (e.getName().equals(VALUES)) {
-				double[] fitnesses;
-				try {
-					fitnesses = parseNumberList(e);
-
-					// confirm that we parsed one fitness value for each possible state.
-					if (fitnesses.length != alphabet.getStateCount()) {
-						throw new ParseException("expected " + alphabet.getStateCount() +" fitnesses, got " + fitnesses.length);
-					}
-				} catch (ParseException e1) {
-					throw new ParseException("Error parsing <" + e.getName() + "> element: " + e1.getMessage());
-				}
-
-				return new PurifyingFitnessValuesModel(fitnesses);
-			} else if (e.getName().equals(MINIMUM_FITNESS)) {
-				try {
-					minimumFitness = parseDouble(e, 0, 1);
-				} catch (ParseException pe) {
-					throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage());
-				}
-			} else if (e.getName().equals(LOW_FITNESS)) {
-				try {
-					lowFitness = parseDouble(e, 0, 1);
-				} catch (ParseException pe) {
-					throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage());
-				}
-			} else {
-				throw new ParseException("Error parsing <" + e.getName() + "> element: <" + e.getName() + "> is unrecognized");
-			}
+                    switch (e.getName()) {
+                        case BETA_DISTIBUTED:
+                            // Carrasco et al (2007)  J Virology 81:12979-12984
+                            double a = 1.151;
+                            double b = 1.709;
+                            double pLethal = 0.4;
+                            
+                            int alphabetSize = alphabet.getStateCount();
+                            int sites = factor.sites.size();
+                            
+                            Element aChild = e.getChild("a");
+                            a = Double.parseDouble(aChild.getText());
+                            Element bChild = e.getChild("b");
+                            b = Double.parseDouble(bChild.getText());
+                            Element pChild = e.getChild("pLethal");
+                            pLethal = Double.parseDouble(pChild.getText());
+                            
+                            return new BetaDistributedPurifyingFitnessModel(a,b, pLethal, alphabetSize, sites);
+                        case VALUES:
+                            double[] fitnesses;
+                            try {
+                                fitnesses = parseNumberList(e);
+                                
+                                // confirm that we parsed one fitness value for each possible state.
+                                if (fitnesses.length != alphabet.getStateCount()) {
+                                    throw new ParseException("expected " + alphabet.getStateCount() +" fitnesses, got " + fitnesses.length);
+                                }
+                            } catch (ParseException e1) {
+                                throw new ParseException("Error parsing <" + e.getName() + "> element: " + e1.getMessage());
+                            }
+                            
+                            return new PurifyingFitnessValuesModel(fitnesses);
+                        case MINIMUM_FITNESS:
+                            try {
+                                minimumFitness = parseDouble(e, 0, 1);
+                            } catch (ParseException pe) {
+                                throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage());
+                            }
+                            break;
+                        case LOW_FITNESS:
+                            try {
+                                lowFitness = parseDouble(e, 0, 1);
+                            } catch (ParseException pe) {
+                                throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage());
+                            }
+                            break;
+                        default:
+                            throw new ParseException("Error parsing <" + e.getName() + "> element: <" + e.getName() + "> is unrecognized");
+                    }
 		}
 		if (minimumFitness == -1 || lowFitness == -1) {
 			throw new ParseException("Error parsing <" + element.getName() + "> element: expecting either a <" + VALUES
@@ -1135,13 +1398,17 @@ private PurifyingFitnessRank parsePurifyingFitnessRank(Element element, FeatureA
 		if (breakTiesElement == null)
 			throw new ParseException("Error parsing <" + element.getName() + "> element: missing <" + BREAK_TIES + ">");
 		String breakTies = breakTiesElement.getTextNormalize();
-		if (breakTies.equals(BREAK_TIES_RANDOM))
-			breakTiesRandom = true;
-		else if (breakTies.equals(BREAK_TIES_ORDERED))
-			breakTiesRandom = false;
-		else
-			throw new ParseException("Error parsing <" + BREAK_TIES + "> element: value must be one of '"
-					+ BREAK_TIES_RANDOM + "' or '" + BREAK_TIES_ORDERED + "'");
+            switch (breakTies) {
+                case BREAK_TIES_RANDOM:
+                    breakTiesRandom = true;
+                    break;
+                case BREAK_TIES_ORDERED:
+                    breakTiesRandom = false;
+                    break;
+                default:
+                    throw new ParseException("Error parsing <" + BREAK_TIES + "> element: value must be one of '"
+                            + BREAK_TIES_RANDOM + "' or '" + BREAK_TIES_ORDERED + "'");
+            }
 
 		for (Object o:element.getChildren()) {
 			Element e = (Element) o;
@@ -1149,30 +1416,35 @@ else if (breakTies.equals(BREAK_TIES_ORDERED))
 			if (e.getName().equals(ORDER)) {
 				String v = e.getTextNormalize();
 
-                if (v.equals(ORDER_OBSERVED_FREQUENCY)) {
-                    order = OrderEnum.OBSERVED;
-                } else if (v.equals(ORDER_CHEMICAL)) {
-                    order = OrderEnum.CLASSES;
-                    orderSetClasses = parseProbableSetClasses(alphabet, CHEMICAL_CLASSES);
-                } else if (v.equals(ORDER_HYDROPATHY)) {
-                    order = OrderEnum.CLASSES;
-                    orderSetClasses = parseProbableSetClasses(alphabet, HYDROPATHY_CLASSES);
-                } else if (v.equals(ORDER_VOLUME)) {
-                    order = OrderEnum.CLASSES;
-                    orderSetClasses = parseProbableSetClasses(alphabet, VOLUME_CLASSES);
-                } else {
-                    if (v.contains("|")) {
-                        order = OrderEnum.CLASSES;
-                        orderSetClasses = parseProbableSetClasses(alphabet, v);
-                    } else {
-                        order = OrderEnum.STATES;
-                        stateOrder = new ArrayList<Byte>();
-
-                        for (int i = 0; i < v.length(); ++i) {
-                            stateOrder.add(alphabet.parse(v.charAt(i)));
-                        }
-                    }
-                }
+                            switch (v) {
+                                case ORDER_OBSERVED_FREQUENCY:
+                                    order = OrderEnum.OBSERVED;
+                                    break;
+                                case ORDER_CHEMICAL:
+                                    order = OrderEnum.CLASSES;
+                                    orderSetClasses = parseProbableSetClasses(alphabet, CHEMICAL_CLASSES);
+                                    break;
+                                case ORDER_HYDROPATHY:
+                                    order = OrderEnum.CLASSES;
+                                    orderSetClasses = parseProbableSetClasses(alphabet, HYDROPATHY_CLASSES);
+                                    break;
+                                case ORDER_VOLUME:
+                                    order = OrderEnum.CLASSES;
+                                    orderSetClasses = parseProbableSetClasses(alphabet, VOLUME_CLASSES);
+                                    break;
+                                default:
+                                    if (v.contains("|")) {
+                                        order = OrderEnum.CLASSES;
+                                        orderSetClasses = parseProbableSetClasses(alphabet, v);
+                                    } else {
+                                        order = OrderEnum.STATES;
+                                        stateOrder = new ArrayList<Byte>();
+                                        
+                                        for (int i = 0; i < v.length(); ++i) {
+                                            stateOrder.add(alphabet.parse(v.charAt(i)));
+                                        }
+                                    }               break;
+                            }
 			} else if (e.getName().equals(PROBABLE_SET)) {
 			    probableNumber = parseInteger(e, 1, alphabet.getStateCount());
 			} else if (!e.getName().equals(BREAK_TIES)) {
@@ -1212,12 +1484,12 @@ else if (breakTies.equals(BREAK_TIES_ORDERED))
 	}
 
 	private List<Set<Byte>> parseProbableSetClasses(SequenceAlphabet alphabet, String str) throws ParseException {
-        Set<Byte> completeCheck = new HashSet<Byte>();
-		List<Set<Byte>> classes = new ArrayList<Set<Byte>>();
+        Set<Byte> completeCheck = new HashSet<>();
+		List<Set<Byte>> classes = new ArrayList<>();
 
 		String[] sets = str.split("\\|");
 		for (String set : sets) {
-			Set<Byte> stateSet = new HashSet<Byte>();
+			Set<Byte> stateSet = new HashSet<>();
 			for (int i = 0; i < set.length(); i++) {
 				byte symbol = alphabet.parse(set.charAt(i));
                 stateSet.add(symbol);
@@ -1237,7 +1509,7 @@ private List<Set<Byte>> parseProbableSetClasses(SequenceAlphabet alphabet, Strin
 	}
 
 	private List<Sequence> parseAlignment(String text) throws ParseException {
-		List<Sequence> result = new ArrayList<Sequence>();
+		List<Sequence> result = new ArrayList<>();
         int firstLength = 0;
 		String[] seqStrings;
 
@@ -1300,7 +1572,7 @@ public double[] parseNumberList(Element element) throws ParseException {
 	}
 
 	private Set<Integer> parseSites(Element element, Feature feature) throws ParseException {
-		Set<Integer> result = new TreeSet<Integer>();
+		Set<Integer> result = new TreeSet<>();
 
 		String sites = element.getTextNormalize();
 		String[] parts = sites.split(",");
@@ -1347,7 +1619,7 @@ private void addSite(Set<Integer> result, int j, Feature feature) throws ParseEx
     }
 
 	private Mutator parseMutator(Element element) throws ParseException {
-		if (element.getChildren().size() == 0) {
+		if (element.getChildren().isEmpty()) {
 			throw new ParseException("Error parsing <" + element.getName() + "> element: the element is empty");
 		}
 
@@ -1366,38 +1638,46 @@ private Mutator parseMutator(Element element) throws ParseException {
 				for (Object o : e.getChildren()) {
 					Element e1 = (Element)o;
 					try {
-						// this should really be a switch statement if we could use a modern java implementation...
-						if (e1.getName().equals(MUTATION_RATE)) {
-							mutationRate = parseDouble(e1, 0.0, Double.MAX_VALUE);
-						} else if (e1.getName().equals(TRANSITION_BIAS)) {
-							transitionBias = parseDouble(e1, 0.0, Double.MAX_VALUE);
-						} else if (e1.getName().equals(RATE_BIAS)) {
-							rateBiases = parseNumberList(e1);
-							if (rateBiases.length != 12) {
-								throw new ParseException("expected 12 rate biases, got " + rateBiases.length);
-							}
-						} else if (e1.getName().equals(INSERT_PROB)) {
-							// http://abacus.gene.ucl.ac.uk/software/indelible/manual/model.shtml#[indelmodel]
-							if (insertProb != -1.0) {
-								throw new ParseException("insertion probability is already set - see previous <" + INSERT_PROB + "> or <" + INDEL_PROB + ">.");
-							}
-							insertProb = parseDouble(e1, 0.0, 1.0);
-						} else if (e1.getName().equals(DELETE_PROB)) {
-							if (deleteProb != -1.0) {
-								throw new ParseException("deletion probability already set - see previous <" + DELETE_PROB + "> or <" + INDEL_PROB + ">.");
-							}
-							deleteProb = parseDouble(e1, 0.0, 1.0);
-						} else if (e1.getName().equals(INDEL_PROB)) {
-							if (insertProb != -1.0 || deleteProb != -1.0) {
-								throw new ParseException("insertion or deletion probability already set - see previous <" + DELETE_PROB + ">, <" + INSERT_PROB + ">, or <" + INDEL_PROB + ">.");
-							}
-							insertProb = parseDouble(e1, 0.0, 1.0);
-							deleteProb = insertProb;
-						} else if (e1.getName().equals(INDEL_MODEL)) {
-							indelModel = parseIndelModel(e1);
-						} else {
-							throw new ParseException("element is unrecognized");
-						}
+                                            // this should really be a switch statement if we could use a modern java implementation...
+                                            switch (e1.getName()) {
+                                                case MUTATION_RATE:
+                                                    mutationRate = parseDouble(e1, 0.0, Double.MAX_VALUE);
+                                                    break;
+                                                case TRANSITION_BIAS:
+                                                    transitionBias = parseDouble(e1, 0.0, Double.MAX_VALUE);
+                                                    break;
+                                                case RATE_BIAS:
+                                                    rateBiases = parseNumberList(e1);
+                                                    if (rateBiases.length != 12) {
+                                                        throw new ParseException("expected 12 rate biases, got " + rateBiases.length);
+                                                    }
+                                                    break;
+                                                case INSERT_PROB:
+                                                    // http://abacus.gene.ucl.ac.uk/software/indelible/manual/model.shtml#[indelmodel]
+                                                    if (insertProb != -1.0) {
+                                                        throw new ParseException("insertion probability is already set - see previous <" + INSERT_PROB + "> or <" + INDEL_PROB + ">.");
+                                                    }
+                                                    insertProb = parseDouble(e1, 0.0, 1.0);
+                                                    break;
+                                                case DELETE_PROB:
+                                                    if (deleteProb != -1.0) {
+                                                        throw new ParseException("deletion probability already set - see previous <" + DELETE_PROB + "> or <" + INDEL_PROB + ">.");
+                                                    }
+                                                    deleteProb = parseDouble(e1, 0.0, 1.0);
+                                                    break;
+                                                case INDEL_PROB:
+                                                    if (insertProb != -1.0 || deleteProb != -1.0) {
+                                                        throw new ParseException("insertion or deletion probability already set - see previous <" + DELETE_PROB + ">, <" + INSERT_PROB + ">, or <" + INDEL_PROB + ">.");
+                                                    }
+                                                    insertProb = parseDouble(e1, 0.0, 1.0);
+                                                    deleteProb = insertProb;
+                                                    break;
+                                                case INDEL_MODEL:
+                                                    indelModel = parseIndelModel(e1);
+                                                    break;
+                                                default:
+                                                    throw new ParseException("element is unrecognized");
+                                            }
 						
 					} catch(ParseException pe) {
 						throw new ParseException("element: <" + e1.getName() + ">: " + pe.getMessage());
@@ -1466,104 +1746,106 @@ private IndelModel parseIndelModel(Element element) throws ParseException {
 
 	private Replicator parseReplicator(Element element) throws ParseException {
 
-		if (element.getChildren().size() == 0) {
+		if (element.getChildren().isEmpty()) {
 			throw new ParseException("Error parsing <" + element.getName() + "> element: the element is empty");
 		}
 
 		Element e = (Element)element.getChildren().get(0);
-		if (e.getName().equals(CLONAL_REPLICATOR)) {
-			return new ClonalReplicator();
-		} else if (e.getName().equals(RECOMBINANT_REPLICATOR_WITH_HOTSPOTS)) {
-			double dualInfectionProbability = -1.0;
-			double recombinationProbability = -1.0;
-
-			for (Object o : e.getChildren()) {
-				Element e1 = (Element)o;
-				if (e1.getName().equals(DUAL_INFECTION_PROBABILITY)) {
-					try {
-						dualInfectionProbability = parseDouble(e1, 0.0, 1.0);
-					} catch (ParseException pe) {
-						throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage());
-					}
-				} else if (e1.getName().equals(RECOMBINATION_PROBABILITY)) {
-					try {
-						recombinationProbability = parseDouble(e1, 0.0, 1.0);
-					} catch (ParseException pe) {
-						throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage());
-					}
-				} else {
-					throw new ParseException("Error parsing <" + e.getName() + "> element: <" + e1.getName() + "> is unrecognized");
-				}
-
-			}
-			if (dualInfectionProbability < 0.0) {
-				throw new ParseException("Error parsing <" + element.getName() + "> element: <" + DUAL_INFECTION_PROBABILITY + "> is missing");
-			}
-
-			if (recombinationProbability < 0.0) {
-				throw new ParseException("Error parsing <" + element.getName() + "> element: <" + RECOMBINATION_PROBABILITY + "> is missing");
-			}
-	        
-			return new RecombinantReplicatorWithHotSpots(dualInfectionProbability, recombinationProbability);
-		} 
-		
-		else if (e.getName().equals(RECOMBINANT_REPLICATOR)) {
-			double dualInfectionProbability = -1.0;
-			double recombinationProbability = -1.0;
-
-			for (Object o : e.getChildren()) {
-				Element e1 = (Element)o;
-				if (e1.getName().equals(DUAL_INFECTION_PROBABILITY)) {
-					try {
-						dualInfectionProbability = parseDouble(e1, 0.0, 1.0);
-					} catch (ParseException pe) {
-						throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage());
-					}
-				} else if (e1.getName().equals(RECOMBINATION_PROBABILITY)) {
-					try {
-						recombinationProbability = parseDouble(e1, 0.0, 1.0);
-					} catch (ParseException pe) {
-						throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage());
-					}
-				} else {
-					throw new ParseException("Error parsing <" + e.getName() + "> element: <" + e1.getName() + "> is unrecognized");
-				}
-
-			}
-			if (dualInfectionProbability < 0.0) {
-				throw new ParseException("Error parsing <" + element.getName() + "> element: <" + DUAL_INFECTION_PROBABILITY + "> is missing");
-			}
-
-			if (recombinationProbability < 0.0) {
-				throw new ParseException("Error parsing <" + element.getName() + "> element: <" + RECOMBINATION_PROBABILITY + "> is missing");
-			}
-	        
-			return new RecombinantReplicator(dualInfectionProbability, recombinationProbability);
-		} 
-		
-		
-			else  {
-			throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized");
-		}
+            switch (e.getName()) {
+                case CLONAL_REPLICATOR:
+                    return new ClonalReplicator();
+                case RECOMBINANT_REPLICATOR_WITH_HOTSPOTS:
+                {
+                    double dualInfectionProbability = -1.0;
+                    double recombinationProbability = -1.0;
+                    
+                    for (Object o : e.getChildren()) {
+                        Element e1 = (Element)o;
+                        if (e1.getName().equals(DUAL_INFECTION_PROBABILITY)) {
+                            try {
+                                dualInfectionProbability = parseDouble(e1, 0.0, 1.0);
+                            } catch (ParseException pe) {
+                                throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage());
+                            }
+                        } else if (e1.getName().equals(RECOMBINATION_PROBABILITY)) {
+                            try {
+                                recombinationProbability = parseDouble(e1, 0.0, 1.0);
+                            } catch (ParseException pe) {
+                                throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage());
+                            }
+                        } else {
+                            throw new ParseException("Error parsing <" + e.getName() + "> element: <" + e1.getName() + "> is unrecognized");
+                        }
+                        
+                    }
+                    if (dualInfectionProbability < 0.0) {
+                        throw new ParseException("Error parsing <" + element.getName() + "> element: <" + DUAL_INFECTION_PROBABILITY + "> is missing");
+                    }
+                    
+                    if (recombinationProbability < 0.0) {
+                        throw new ParseException("Error parsing <" + element.getName() + "> element: <" + RECOMBINATION_PROBABILITY + "> is missing");
+                    }
+                    
+                    return new RecombinantReplicatorWithHotSpots(dualInfectionProbability, recombinationProbability);
+                }
+                case RECOMBINANT_REPLICATOR:
+                {
+                    double dualInfectionProbability = -1.0;
+                    double recombinationProbability = -1.0;
+                    
+                    for (Object o : e.getChildren()) {
+                        Element e1 = (Element)o;
+                        switch (e1.getName()) {
+                            case DUAL_INFECTION_PROBABILITY:
+                                try {
+                                    dualInfectionProbability = parseDouble(e1, 0.0, 1.0);
+                                } catch (ParseException pe) {
+                                    throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage());
+                                }   break;
+                            case RECOMBINATION_PROBABILITY:
+                                try {
+                                    recombinationProbability = parseDouble(e1, 0.0, 1.0);
+                                } catch (ParseException pe) {
+                                    throw new ParseException("Error parsing <" + e.getName() + "> element: " + pe.getMessage());
+                                }   break;
+                            default:
+                                throw new ParseException("Error parsing <" + e.getName() + "> element: <" + e1.getName() + "> is unrecognized");
+                        }
+                        
+                    }
+                    if (dualInfectionProbability < 0.0) {
+                        throw new ParseException("Error parsing <" + element.getName() + "> element: <" + DUAL_INFECTION_PROBABILITY + "> is missing");
+                    }
+                    
+                    if (recombinationProbability < 0.0) {
+                        throw new ParseException("Error parsing <" + element.getName() + "> element: <" + RECOMBINATION_PROBABILITY + "> is missing");
+                    }
+                    
+                    return new RecombinantReplicator(dualInfectionProbability, recombinationProbability);
+                }
+                default:
+                    throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized");
+            }
 
 	}
 
 	private GenePool parseGenePool(Element element) throws ParseException {
 
-		if (element.getChildren().size() == 0) {
+		if (element.getChildren().isEmpty()) {
 			throw new ParseException("Error parsing <" + element.getName() + "> element: the element is empty");
 		}
 
 		Element e = (Element)element.getChildren().get(0);
-		if (e.getName().equals(SIMPLE_GENE_POOL)) {
-			// SimpleGenome/GenePool uses a simple format where the whole sequence is stored
-			return new SimpleGenePool();
-		} else if (e.getName().equals(COMPACT_GENE_POOL)) {
-			// CompactGenome/GenePool uses a compact format where only changes are stored
-			return new CompactGenePool();
-		} else {
-			throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized");
-		}
+            switch (e.getName()) {
+                case SIMPLE_GENE_POOL:
+                    // SimpleGenome/GenePool uses a simple format where the whole sequence is stored
+                    return new SimpleGenePool();
+                case COMPACT_GENE_POOL:
+                    // CompactGenome/GenePool uses a compact format where only changes are stored
+                    return new CompactGenePool();
+                default:
+                    throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e.getName() + "> is unrecognized");
+            }
 
 	}
 
@@ -1592,23 +1874,28 @@ private void parseSampler(Element element, SamplingSchedule samplingSchedule) th
 
 		for (Object o : element.getChildren()) {
 			Element e1 = (Element)o;
-			if (e1.getName().equals(AT_FREQUENCY)) {
-				try {
-					frequency = parseInteger(e1, 1, Integer.MAX_VALUE);
-				} catch (ParseException pe) {
-					throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage());
-				}
-			} else if (e1.getName().equals(AT_GENERATION)) {
-				try {
-					generation = parseInteger(e1, 1, Integer.MAX_VALUE);
-				} catch (ParseException pe) {
-					throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage());
-				}
-			} else if (e1.getName().equals(FILE_NAME)) {
-				fileName = e1.getTextNormalize();
-			} else {
-				// skip over it
-			}
+                    switch (e1.getName()) {
+                        case AT_FREQUENCY:
+                            try {
+                                frequency = parseInteger(e1, 1, Integer.MAX_VALUE);
+                            } catch (ParseException pe) {
+                                throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage());
+                            }
+                            break;
+                        case AT_GENERATION:
+                            try {
+                                generation = parseInteger(e1, 1, Integer.MAX_VALUE);
+                            } catch (ParseException pe) {
+                                throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage());
+                            }
+                            break;
+                        case FILE_NAME:
+                            fileName = e1.getTextNormalize();
+                            break;
+                    // skip over it
+                        default:
+                            break;
+                    }
 
 		}
 
@@ -1624,21 +1911,30 @@ private void parseSampler(Element element, SamplingSchedule samplingSchedule) th
 
 		for (Object o : element.getChildren()) {
 			Element e1 = (Element)o;
-			if (e1.getName().equals(ALIGNMENT)) {
-				sampler = parseAlignmentSampler(e1, samplingSchedule, fileName);
-			} else if (e1.getName().equals(GENOMEDESCRIPTION)) {
-				sampler = parseGenomeDescriptionSampler(e1, samplingSchedule, fileName);
-			} else if (e1.getName().equals(TREE)) {
-				sampler = parseTreeSampler(e1, samplingSchedule, fileName);
-			} else if (e1.getName().equals(ALLELE_FREQUENCY)) {
-				sampler = parseAlleleFrequencySampler(e1, samplingSchedule, fileName);
-			} else if (e1.getName().equals(STATISTICS)) {
-				sampler = parseStatisticsSampler(e1, samplingSchedule, fileName);
-			} else if (e1.getName().equals(AT_FREQUENCY) || e1.getName().equals(AT_GENERATION) || e1.getName().equals(FILE_NAME)) {
-				// skip over it
-			} else {
-				throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized");
-			}
+                    switch (e1.getName()) {
+                        case ALIGNMENT:
+                            sampler = parseAlignmentSampler(e1, samplingSchedule, fileName);
+                            break;
+                        case GENOMEDESCRIPTION:
+                            sampler = parseGenomeDescriptionSampler(e1, samplingSchedule, fileName);
+                            break;
+                        case TREE:
+                            sampler = parseTreeSampler(e1, samplingSchedule, fileName);
+                            break;
+                        case ALLELE_FREQUENCY:
+                            sampler = parseAlleleFrequencySampler(e1, samplingSchedule, fileName);
+                            break;
+                        case STATISTICS:
+                            sampler = parseStatisticsSampler(e1, samplingSchedule, fileName);
+                            break;
+                    // skip over it
+                        case AT_FREQUENCY:
+                        case AT_GENERATION:
+                        case FILE_NAME:
+                            break;
+                        default:
+                            throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized");
+                    }
 
 		}
 
@@ -1664,31 +1960,35 @@ private Sampler parseGenomeDescriptionSampler(Element element, SamplingSchedule
 
 		for (Object o : element.getChildren()) {
 			Element e1 = (Element)o;
-			if (e1.getName().equals(SAMPLE_SIZE)) {
-				try {
-					sampleSize = parseInteger(e1, 1, Integer.MAX_VALUE);
-				} catch (ParseException pe) {
-					throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage());
-				}
-			} else if (e1.getName().equals(SCHEDULE)) {
-				String[] values = e1.getTextTrim().split("\\s+");
-				schedule = new TreeMap<Integer,Integer>();
-				try {
-					for (int i = 0; i<values.length/2; ++i) {
-						int g = Integer.parseInt(values[i*2]);
-						int n = Integer.parseInt(values[i*2 + 1]);
-
-						schedule.put(g, n);
-					}
-				} catch (NumberFormatException e) {
-					throw new ParseException("Error parsing <" + element.getName() + "> element: "
-							+ e.getMessage());
-				}
-			} else if (e1.getName().equals(LABEL)) {
-				label = e1.getTextNormalize();
-			} else {
-				throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized");
-			}
+                    switch (e1.getName()) {
+                        case SAMPLE_SIZE:
+                            try {
+                                sampleSize = parseInteger(e1, 1, Integer.MAX_VALUE);
+                            } catch (ParseException pe) {
+                                throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage());
+                            }
+                            break;
+                        case SCHEDULE:
+                            String[] values = e1.getTextTrim().split("\\s+");
+                            schedule = new TreeMap<>();
+                            try {
+                                for (int i = 0; i<values.length/2; ++i) {
+                                    int g = Integer.parseInt(values[i*2]);
+                                    int n = Integer.parseInt(values[i*2 + 1]);
+                                    
+                                    schedule.put(g, n);
+                                }
+                            } catch (NumberFormatException e) {
+                                throw new ParseException("Error parsing <" + element.getName() + "> element: "
+                                        + e.getMessage());
+                            }
+                            break;
+                        case LABEL:
+                            label = e1.getTextNormalize();
+                            break;
+                        default:
+                            throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized");
+                    }
 
 		}
 
@@ -1713,51 +2013,57 @@ private Sampler parseAlignmentSampler(Element element, SamplingSchedule sampling
 
 		for (Object o : element.getChildren()) {
 			Element e1 = (Element)o;
-			if (e1.getName().equals(SAMPLE_SIZE)) {
-				try {
-					sampleSize = parseInteger(e1, 1, Integer.MAX_VALUE);
-				} catch (ParseException pe) {
-					throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage());
-				}
-			} else if (e1.getName().equals(SCHEDULE)) {
-				String[] values = e1.getTextTrim().split("\\s+");
-				schedule = new TreeMap<Integer,Integer>();
-				try {
-					for (int i = 0; i<values.length/2; ++i) {
-						int g = Integer.parseInt(values[i*2]);
-						int n = Integer.parseInt(values[i*2 + 1]);
-
-						schedule.put(g, n);
-					}
-				} catch (NumberFormatException e) {
-					throw new ParseException("Error parsing <" + element.getName() + "> element: "
-							+ e.getMessage());
-				}
-			} else if (e1.getName().equals(FORMAT)) {
-				String formatText = e1.getTextNormalize();
-				if (formatText.equalsIgnoreCase("NEXUS")) {
-					format = AlignmentSampler.Format.NEXUS;
-				} else if (formatText.equalsIgnoreCase("FASTA")) {
-					format = AlignmentSampler.Format.FASTA;
-				} else if (formatText.equalsIgnoreCase("XML")) {
-					format = AlignmentSampler.Format.XML;
-				} else {
-					throw new ParseException("Error parsing <" + element.getName() + "> element: <" + FORMAT + "> value of " + formatText + " is unrecognized");
-				}
-			} else if (e1.getName().equals(CONSENSUS)) {
-				String booleanText = e1.getTextNormalize();
-				if (booleanText.equalsIgnoreCase("TRUE")) {
-					consensus = true;
-				} else if (booleanText.equalsIgnoreCase("FALSE")) {
-					consensus = false;
-				} else {
-					throw new ParseException("Error parsing <" + element.getName() + "> element: <" + CONSENSUS + "> value " + booleanText + " is unrecognized");
-				}
-			} else if (e1.getName().equals(LABEL)) {
-				label = e1.getTextNormalize();
-			} else {
-				throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized");
-			}
+                    switch (e1.getName()) {
+                        case SAMPLE_SIZE:
+                            try {
+                                sampleSize = parseInteger(e1, 1, Integer.MAX_VALUE);
+                            } catch (ParseException pe) {
+                                throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage());
+                            }
+                            break;
+                        case SCHEDULE:
+                            String[] values = e1.getTextTrim().split("\\s+");
+                            schedule = new TreeMap<>();
+                            try {
+                                for (int i = 0; i<values.length/2; ++i) {
+                                    int g = Integer.parseInt(values[i*2]);
+                                    int n = Integer.parseInt(values[i*2 + 1]);
+                                    
+                                    schedule.put(g, n);
+                                }
+                            } catch (NumberFormatException e) {
+                                throw new ParseException("Error parsing <" + element.getName() + "> element: "
+                                        + e.getMessage());
+                            }
+                            break;
+                        case FORMAT:
+                            String formatText = e1.getTextNormalize();
+                            if (formatText.equalsIgnoreCase("NEXUS")) {
+                                format = AlignmentSampler.Format.NEXUS;
+                            } else if (formatText.equalsIgnoreCase("FASTA")) {
+                                format = AlignmentSampler.Format.FASTA;
+                            } else if (formatText.equalsIgnoreCase("XML")) {
+                                format = AlignmentSampler.Format.XML;
+                            } else {
+                                throw new ParseException("Error parsing <" + element.getName() + "> element: <" + FORMAT + "> value of " + formatText + " is unrecognized");
+                            }
+                            break;
+                        case CONSENSUS:
+                            String booleanText = e1.getTextNormalize();
+                            if (booleanText.equalsIgnoreCase("TRUE")) {
+                                consensus = true;
+                            } else if (booleanText.equalsIgnoreCase("FALSE")) {
+                                consensus = false;
+                            } else {
+                                throw new ParseException("Error parsing <" + element.getName() + "> element: <" + CONSENSUS + "> value " + booleanText + " is unrecognized");
+                            }
+                            break;
+                        case LABEL:
+                            label = e1.getTextNormalize();
+                            break;
+                        default:
+                            throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized");
+                    }
 
 		}
 
@@ -1778,40 +2084,45 @@ private Sampler parseTreeSampler(Element element, SamplingSchedule samplingSched
 
 		for (Object o : element.getChildren()) {
 			Element e1 = (Element)o;
-			if (e1.getName().equals(SAMPLE_SIZE)) {
-				try {
-					sampleSize = parseInteger(e1, 1, Integer.MAX_VALUE);
-				} catch (ParseException pe) {
-					throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage());
-				}
-			} else if (e1.getName().equals(SCHEDULE)) {
-				String[] values = e1.getTextTrim().split("\\s+");
-				schedule = new TreeMap<Integer,Integer>();
-				try {
-					for (int i = 0; i<values.length/2; ++i) {
-						int g = Integer.parseInt(values[i*2]);
-						int n = Integer.parseInt(values[i*2 + 1]);
-
-						schedule.put(g, n);
-					}
-				} catch (NumberFormatException e) {
-					throw new ParseException("Error parsing <" + element.getName() + "> element: "
-							+ e.getMessage());
-				}
-			} else if (e1.getName().equals(FORMAT)) {
-				String formatText = e1.getTextNormalize();
-				if (formatText.equalsIgnoreCase("NEXUS")) {
-					format = TreeSampler.Format.NEXUS;
-				} else if (formatText.equalsIgnoreCase("NEWICK")) {
-					format = TreeSampler.Format.NEWICK;
-				} else {
-					throw new ParseException("Error parsing <" + element.getName() + "> element: <" + FORMAT + "> value of " + formatText + " is unrecognized");
-				}
-			} else if (e1.getName().equals(LABEL)) {
-				label = e1.getTextNormalize();
-			} else {
-				throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized");
-			}
+                    switch (e1.getName()) {
+                        case SAMPLE_SIZE:
+                            try {
+                                sampleSize = parseInteger(e1, 1, Integer.MAX_VALUE);
+                            } catch (ParseException pe) {
+                                throw new ParseException("Error parsing <" + element.getName() + "> element: " + pe.getMessage());
+                            }
+                            break;
+                        case SCHEDULE:
+                            String[] values = e1.getTextTrim().split("\\s+");
+                            schedule = new TreeMap<Integer,Integer>();
+                            try {
+                                for (int i = 0; i<values.length/2; ++i) {
+                                    int g = Integer.parseInt(values[i*2]);
+                                    int n = Integer.parseInt(values[i*2 + 1]);
+                                    
+                                    schedule.put(g, n);
+                                }
+                            } catch (NumberFormatException e) {
+                                throw new ParseException("Error parsing <" + element.getName() + "> element: "
+                                        + e.getMessage());
+                            }
+                            break;
+                        case FORMAT:
+                            String formatText = e1.getTextNormalize();
+                            if (formatText.equalsIgnoreCase("NEXUS")) {
+                                format = TreeSampler.Format.NEXUS;
+                            } else if (formatText.equalsIgnoreCase("NEWICK")) {
+                                format = TreeSampler.Format.NEWICK;
+                            } else {
+                                throw new ParseException("Error parsing <" + element.getName() + "> element: <" + FORMAT + "> value of " + formatText + " is unrecognized");
+                            }
+                            break;
+                        case LABEL:
+                            label = e1.getTextNormalize();
+                            break;
+                        default:
+                            throw new ParseException("Error parsing <" + element.getName() + "> element: <" + e1.getName() + "> is unrecognized");
+                    }
 
 		}
 
diff --git a/src/santa/simulator/Virus.java b/src/santa/simulator/Virus.java
index 424b7c4..e32cef2 100644
--- a/src/santa/simulator/Virus.java
+++ b/src/santa/simulator/Virus.java
@@ -1,6 +1,8 @@
 
 package santa.simulator;
 
+import java.util.ArrayList;
+import santa.simulator.compartments.Compartment;
 import santa.simulator.genomes.Genome;
 
 /**
@@ -16,6 +18,10 @@ public Virus() {
     public Virus(Genome genome, Virus parent) {
         this.genome = genome;
         this.parent = parent;
+        if (parent != null) {
+            this.age = parent.age;
+            this.lastCompartment = parent.lastCompartment;
+        }
     }
 
     public Genome getGenome() {
@@ -34,12 +40,21 @@ public double getFitness() {
 		return genome.getFitness();
 	}
 
+    public int getAge() {
+        return age;
+    }
+        
+    public Compartment getLastCompartment() {
+        return lastCompartment;
+    }
+        
     public void setGenome(Genome genome) {
         this.genome = genome;
     }
 
     public void setParent(Virus parent) {
         this.parent = parent;
+        setAge(parent.age);
     }
 
     public int getOffspringCount() {
@@ -49,9 +64,18 @@ public int getOffspringCount() {
     public void setOffspringCount(int offspringCount) {
         this.offspringCount = offspringCount;
     }
-
+    
+    public void setAge(int age) {
+        this.age = age;
+    }
+    
+    public void setLastCompartment(Compartment lastCompartment) {
+        this.lastCompartment = lastCompartment;
+    }
+    
     private Genome genome = null;
     private Virus parent = null;
     private int offspringCount = 0;
-
+    private int age = 0;
+    private Compartment lastCompartment = null;
 }
diff --git a/src/santa/simulator/compartments/Compartment.java b/src/santa/simulator/compartments/Compartment.java
new file mode 100644
index 0000000..7bbced2
--- /dev/null
+++ b/src/santa/simulator/compartments/Compartment.java
@@ -0,0 +1,118 @@
+package santa.simulator.compartments;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.logging.Logger;
+import santa.simulator.EventLogger;
+import santa.simulator.Random;
+import santa.simulator.genomes.GenePool;
+import santa.simulator.genomes.GenomeDescription;
+import santa.simulator.genomes.Sequence;
+import santa.simulator.phylogeny.Phylogeny;
+import santa.simulator.population.Population;
+import santa.simulator.population.PopulationGrowth;
+import santa.simulator.samplers.SamplingSchedule;
+import santa.simulator.selectors.Selector;
+
+/**
+ *
+ * @author Bradley R. Jones
+ */
+public class Compartment {
+    private int populationSize;
+    private String name;
+    private Compartment.InoculumType inoculumType;
+    private GenePool genePool;
+    private List<CompartmentEpoch> epochs;
+    private Selector selector;
+    private SamplingSchedule samplingSchedule;
+    private Population population;
+
+    	public enum InoculumType {
+		NONE,
+		CONSENSUS,
+		RANDOM,
+		ALL
+	};
+	
+	//Default constructor (dynamic)
+    public Compartment (
+            String name,
+            int populationSize,
+            Selector selector,
+            PopulationGrowth growth,
+            InoculumType inoculumType,
+            GenePool genePool,
+            List<CompartmentEpoch> epochs,
+            SamplingSchedule samplingSchedule) {
+
+        this.name = name;
+        this.populationSize = populationSize;
+        this.inoculumType = inoculumType;
+        this.epochs = epochs;
+        this.samplingSchedule = samplingSchedule;
+        this.genePool = genePool;
+        this.selector = selector;
+
+        population = new Population(genePool, selector, growth, samplingSchedule.isSamplingTrees() ? new Phylogeny(populationSize) : null);
+    }
+    
+    public void initalize(int replicate, Logger logger) {
+        samplingSchedule.initialize(replicate);
+
+        EventLogger.setReplicate(replicate);
+
+        logger.finer("Initializing population: " + populationSize + " viruses.");
+
+	    List<Sequence> inoculum = new ArrayList<>();
+	    if (null == inoculumType) { // NONE
+                // do nothing
+            } else switch (inoculumType) {
+            case CONSENSUS:
+                inoculum.add(GenomeDescription.getConsensus());
+                break;
+            case ALL:
+                inoculum.addAll(GenomeDescription.getSequences());
+                break;
+            case RANDOM:
+                List<Sequence> sequences = GenomeDescription.getSequences();
+                if (sequences.size() == 1) {
+                    inoculum.add(sequences.get(0));
+                } else {
+                    inoculum.add(sequences.get(Random.nextInt(0, sequences.size() - 1)));
+                }
+                break;
+            default:
+                break;
+        }
+        population.initialize(inoculum, populationSize);
+    }
+    
+    public void cleanup(int replicate, Logger logger) {
+        samplingSchedule.cleanUp();
+    }
+    
+    public GenePool getGenePool() {
+        return genePool;
+    }
+
+    public Population getPopulation() {
+        return population;
+    }
+
+    public int getPopulationSize() {
+        return populationSize;
+    }
+
+    public SamplingSchedule getSamplingSchedule() {
+        return samplingSchedule;
+    }
+    
+    public String getName() {
+        return name;
+    }
+    
+    public List<CompartmentEpoch> getEpochs() {
+        return epochs;
+    }
+}
diff --git a/src/santa/simulator/compartments/CompartmentEpoch.java b/src/santa/simulator/compartments/CompartmentEpoch.java
new file mode 100644
index 0000000..7a80a41
--- /dev/null
+++ b/src/santa/simulator/compartments/CompartmentEpoch.java
@@ -0,0 +1,122 @@
+
+package santa.simulator.compartments;
+
+
+import java.util.logging.Logger;
+import santa.simulator.fitness.FitnessFunction;
+import santa.simulator.genomes.GenePool;
+import santa.simulator.mutators.Mutator;
+import santa.simulator.population.Population;
+import santa.simulator.replicators.Replicator;
+import santa.simulator.samplers.SamplingSchedule;
+
+/* 
+ * @author Andrew Rambaut
+ * @author Bradley R. Jones
+*/
+public class CompartmentEpoch {
+    private String name;
+    private int generationCount;
+    private FitnessFunction fitnessFunction;
+    private Mutator mutator;
+    private Replicator replicator;
+
+    public CompartmentEpoch(String name, int generationCount,
+            FitnessFunction fitnessFunction, Mutator mutator,
+            Replicator replicator) {
+        this.name = name;
+        this.generationCount = generationCount;
+        this.fitnessFunction = fitnessFunction;
+        this.mutator = mutator;
+        this.replicator = replicator;
+    }
+
+    @SuppressWarnings("empty-statement")
+    public int step(Compartment compartment, Logger logger, int startGeneration, int generation) {
+        Population population = compartment.getPopulation();
+        GenePool genePool = compartment.getGenePool();
+        SamplingSchedule samplingSchedule = compartment.getSamplingSchedule();
+        
+        if (population.getCurrentGeneration().isEmpty())
+            return 0;
+        
+        fitnessFunction.updateGeneration(generation, population);
+
+        if (generation == startGeneration) {
+            // adapt to this epoch, and the new generation
+            population.updateAllFitnesses(fitnessFunction);
+            
+            System.err.println("Initial population:" +
+                    " compartment = " + compartment.getName() +
+                    ", population = " + population.getCurrentGeneration().size() +
+                    ", fitness = " + population.getMeanFitness() +
+                ", distance = " + population.getMeanDistance() +
+                ", max freq = " + population.getMaxFrequency() +
+                ", genepool size = " + genePool.getUniqueGenomeCount() +
+                " (" + genePool.getUnusedGenomeCount() + " available)");                
+        }
+
+        population.selectNextGeneration(generation, replicator, mutator, fitnessFunction);
+        
+        if (population.getCurrentGeneration().isEmpty())
+            return 0;
+        
+        if (generation % 10 == 0) {
+            if (population.getPhylogeny() != null)
+                population.getPhylogeny().pruneDeadLineages();
+
+            System.err.print("Generation " + generation + 
+                    ": compartment = " + compartment.getName() +
+                    ", population = " + population.getCurrentGeneration().size() +
+                    ", fitness = " + population.getMeanFitness() +
+                ", distance = " + population.getMeanDistance() +
+                ", max freq = " + population.getMaxFrequency() +
+                ", genepool size = " + genePool.getUniqueGenomeCount() +
+                " (" + genePool.getUnusedGenomeCount() + " available)");
+            if (population.getPhylogeny() != null) {
+                population.getPhylogeny().pruneDeadLineages();
+                System.err.println(", phylogeny size = " + population.getPhylogeny().getSize() +
+                    " (used = " + population.getPhylogeny().getLineageCount()+ ")" +
+                    ", tmrca = " + population.getPhylogeny().getMRCA().getGeneration() );
+            } else
+                System.err.println();
+        } else {
+            logger.finest("Generation " + generation + 
+                    ": compartment = " + compartment.getName() +
+                    ", population = " + population.getCurrentGeneration().size() +
+                    " fitness = " + population.getMeanFitness() +
+                ", distance = " + population.getMeanDistance() +
+            	", max freq = " + population.getMaxFrequency() +
+            	", genepool size= " + genePool.getUniqueGenomeCount() +
+            	"(" + genePool.getUnusedGenomeCount() + " available)");                
+        }
+                
+        samplingSchedule.doSampling(generation, population);
+        
+        return population.getPopulationSize();
+    }
+
+    public FitnessFunction getFitnessFunction() {
+        return fitnessFunction;
+    }
+
+    public Mutator getMutator() {
+        return mutator;
+    }
+
+    public Replicator getReplicator() {
+        return replicator;
+    }
+    
+    public int getGenerationCount() {
+        return generationCount;
+    }
+    
+    public String getName() {
+        return name;
+    }
+    
+    public void setGenerationCount(int generationCount) {
+        this.generationCount = generationCount;
+    }
+}
diff --git a/src/santa/simulator/compartments/Compartments.java b/src/santa/simulator/compartments/Compartments.java
new file mode 100644
index 0000000..3065e3e
--- /dev/null
+++ b/src/santa/simulator/compartments/Compartments.java
@@ -0,0 +1,33 @@
+package santa.simulator.compartments;
+
+import java.util.Iterator;
+import java.util.List;
+
+/**
+ *
+ * @author Bradley R. Jones
+ */
+public class Compartments implements Iterable<Compartment> {
+    private Transfer transfer;
+    private List<Compartment> compartments;
+    private int numCompartments;
+    
+    public Compartments(List<Compartment> compartments, Transfer transfer) {
+        this.compartments = compartments;
+        this.numCompartments = compartments.size();
+        this.transfer = transfer;
+    }
+    
+    public void genomeTransfer(int generation, List<CompartmentEpoch> currentEpochs) {
+        transfer.genomeTransfer(compartments, generation, currentEpochs);
+    }
+    
+    public int getNumCompartments() {
+        return numCompartments;
+    }
+
+    @Override
+    public Iterator<Compartment> iterator() {
+        return compartments.iterator();
+    }
+}
diff --git a/src/santa/simulator/compartments/DoubleProb.java b/src/santa/simulator/compartments/DoubleProb.java
new file mode 100644
index 0000000..f2aca2c
--- /dev/null
+++ b/src/santa/simulator/compartments/DoubleProb.java
@@ -0,0 +1,19 @@
+package santa.simulator.compartments;
+
+import santa.simulator.Virus;
+
+/**
+ *
+ * @author Bradley R. Jones
+ */
+public class DoubleProb implements TransferProb {
+    private double transferRate;
+    
+    public DoubleProb(double transferRate) {
+        this.transferRate = transferRate;
+    }
+    
+    public double getProb(Virus virus, int generation) {
+        return transferRate;
+    }
+}
diff --git a/src/santa/simulator/compartments/FitnessProb.java b/src/santa/simulator/compartments/FitnessProb.java
new file mode 100644
index 0000000..f28f887
--- /dev/null
+++ b/src/santa/simulator/compartments/FitnessProb.java
@@ -0,0 +1,24 @@
+package santa.simulator.compartments;
+
+import santa.simulator.Virus;
+import santa.simulator.fitness.FitnessFunction;
+import santa.simulator.genomes.Genome;
+
+/**
+ *
+ * @author Bradley R. Jones
+ */
+public class FitnessProb implements TransferProb {
+    public FitnessFunction fitness;
+    
+    public FitnessProb(FitnessFunction fitness) {
+        this.fitness = fitness;
+    }
+    
+    public double getProb(Virus virus, int generation) {
+        Genome genome = virus.getGenome().copy();
+        fitness.computeLogFitness(genome);
+        
+        return genome.getFitness();
+    }
+}
diff --git a/src/santa/simulator/compartments/MatrixTransfer.java b/src/santa/simulator/compartments/MatrixTransfer.java
new file mode 100644
index 0000000..fd2ec9e
--- /dev/null
+++ b/src/santa/simulator/compartments/MatrixTransfer.java
@@ -0,0 +1,99 @@
+package santa.simulator.compartments;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.TreeSet;
+import santa.simulator.Random;
+import santa.simulator.Virus;
+import santa.simulator.fitness.FitnessFunction;
+import santa.simulator.genomes.GenePool;
+import santa.simulator.genomes.Genome;
+import santa.simulator.genomes.Mutation;
+
+/**
+ *
+ * @author Bradley R. Jones
+ */
+public class MatrixTransfer implements Transfer {
+
+    private TransferProb[][] transferProbs;
+    private int numCompartments;
+
+    public MatrixTransfer(List<TransferProb> transferRates, int numCompartments) {
+        this.numCompartments = numCompartments;
+        this.transferProbs = new TransferProb[this.numCompartments][this.numCompartments];
+
+        for (int i = 0; i < transferRates.size(); i++) {
+            this.transferProbs[i / this.numCompartments][i % this.numCompartments] = transferRates.get(i);
+        }
+    }
+
+    @Override
+    public void genomeTransfer(List<Compartment> compartments, int generation, List<CompartmentEpoch> currentEpochs) {
+        if (numCompartments > 1) {
+            ArrayList< ArrayList<Virus>> allVirusesToAdd = new ArrayList<>(numCompartments);
+
+            for (int i = 0; i < numCompartments; i++) {
+                allVirusesToAdd.add(new ArrayList<Virus>());
+            }
+
+            for (int compartmentFromID = 0; compartmentFromID < numCompartments; compartmentFromID++) {
+                Compartment migrator = compartments.get(compartmentFromID);
+                List<Virus> viruses = migrator.getPopulation().getCurrentGeneration();
+                GenePool genePool = migrator.getGenePool();
+
+                for (int virusID = 0; virusID < viruses.size(); virusID++) {
+                    double transfer = Random.nextUniform(0, 1);
+                    Virus virus = viruses.get(virusID);
+
+                    for (int compartmentToID = 0; compartmentToID < numCompartments; compartmentToID++) {
+                        double prob = transferProbs[compartmentFromID][compartmentToID].getProb(virus, generation);
+                        
+                        if (transfer < prob) {
+                            if (compartmentFromID != compartmentToID) {
+                                ArrayList<Virus> virusesToAdd = allVirusesToAdd.get(compartmentToID);
+                                Genome genome = virus.getGenome();
+
+                                // record compartment entry
+                                virus.setAge(generation);
+                                virus.setLastCompartment(migrator);
+
+                                virusesToAdd.add(virus);
+                                viruses.remove(virusID);
+                                genePool.killGenome(genome);
+
+                                virusID--;
+                            }
+
+                            break;
+                        } else {
+                            transfer -= prob;
+                        }
+                    }
+                }
+            }
+
+            for (int compartmentToID = 0; compartmentToID < numCompartments; compartmentToID++) {
+                List<Virus> virusesToAdd = allVirusesToAdd.get(compartmentToID);
+
+                if (!virusesToAdd.isEmpty()) {
+                    FitnessFunction fitnessFunction = currentEpochs.get(compartmentToID).getFitnessFunction();
+                    GenePool compartmentGenePool = compartments.get(compartmentToID).getGenePool();
+                    List<Virus> viruses = compartments.get(compartmentToID).getPopulation().getCurrentGeneration();
+
+                    // fix later to remove create less genomes
+                    for (Virus v : virusesToAdd) {
+                        Genome genome = v.getGenome();
+                        Genome newGenome = compartmentGenePool.createGenome(genome.getSequence(), genome.getDescription());
+
+                        v.setGenome(newGenome);
+                        fitnessFunction.computeLogFitness(newGenome);
+                        compartmentGenePool.duplicateGenome(newGenome, new TreeSet<Mutation>(), fitnessFunction);
+                    }
+
+                    viruses.addAll(virusesToAdd);
+                }
+            }
+        }
+    }
+}
diff --git a/src/santa/simulator/compartments/TimedTransfer.java b/src/santa/simulator/compartments/TimedTransfer.java
new file mode 100644
index 0000000..84a517d
--- /dev/null
+++ b/src/santa/simulator/compartments/TimedTransfer.java
@@ -0,0 +1,110 @@
+package santa.simulator.compartments;
+
+import java.util.List;
+import java.util.TreeSet;
+import santa.simulator.Random;
+import santa.simulator.Virus;
+import santa.simulator.fitness.FitnessFunction;
+import santa.simulator.genomes.GenePool;
+import santa.simulator.genomes.Genome;
+import santa.simulator.genomes.Mutation;
+
+/**
+ *
+ * @author Bradley R. Jones
+ */
+public class TimedTransfer implements Transfer {
+    private List<TransferEvent> transferEvents;
+    private int currentIndex = 0;
+
+    public TimedTransfer(List<TransferEvent> transferEvents) {
+        this.transferEvents = transferEvents;
+        
+        // sort in order of generation
+        transferEvents.sort(null);
+    }
+    
+    public void genomeTransfer(List<Compartment> compartments, int generation, List<CompartmentEpoch> currentEpochs) {
+        TransferEvent nextEvent = null;
+        
+        if (currentIndex < transferEvents.size())
+            nextEvent = transferEvents.get(currentIndex);
+        
+        while (nextEvent != null && nextEvent.getGeneration() == generation) {
+            Compartment fromCompartment = compartments.get(nextEvent.getFromCompartmentIndex());
+            Compartment toCompartment = compartments.get(nextEvent.getToCompartmentIndex());
+            List<Virus> fromViruses = fromCompartment.getPopulation().getCurrentGeneration();
+            List<Virus> toViruses = toCompartment.getPopulation().getCurrentGeneration();
+            GenePool toGenePool = fromCompartment.getGenePool();
+            GenePool fromGenePool = toCompartment.getGenePool();
+            FitnessFunction fitness = currentEpochs.get(nextEvent.getToCompartmentIndex()).getFitnessFunction();
+            
+            Object[] virusesToTransfer = Random.nextSample(fromViruses, nextEvent.getAmountToTransfer());
+             
+            for (Object o: virusesToTransfer) {
+                 Virus virus = (Virus)o;
+                 Genome genome = virus.getGenome();
+                 
+                 fromViruses.remove(virus);
+                 fromGenePool.killGenome(genome);
+                                  
+                 virus.setAge(generation);
+                 virus.setLastCompartment(fromCompartment);
+                 
+                 Genome newGenome = toGenePool.createGenome(genome.getSequence(), genome.getDescription());
+                 virus.setGenome(newGenome);
+                 fitness.computeLogFitness(newGenome);
+                 fromGenePool.duplicateGenome(newGenome, new TreeSet<Mutation>(), fitness);
+                 toViruses.add(virus);
+            }
+            
+            if (++currentIndex < transferEvents.size())
+                nextEvent = transferEvents.get(currentIndex);
+            else
+                nextEvent = null;
+        }
+    }
+
+    public static class TransferEvent implements Comparable<TransferEvent> {
+        private String fromCompartment;
+        private String toCompartment;
+        private int fromCompartmentIndex;
+        private int toCompartmentIndex;
+        private int generation;
+        private int amountToTransfer;
+        
+        public TransferEvent(String fromCompartment, String toCompartment, int generation, int amountToTransfer) {
+            this.fromCompartment = fromCompartment;
+            this.toCompartment = toCompartment;
+            this.generation = generation;
+            this.amountToTransfer = amountToTransfer;
+        }
+        
+        public boolean findCompartmentIndices(List<String> compartmentNames) {
+            fromCompartmentIndex = compartmentNames.indexOf(fromCompartment);
+            toCompartmentIndex = compartmentNames.indexOf(toCompartment);
+            
+            return fromCompartmentIndex != -1 && toCompartmentIndex != -1;
+        }
+        
+        public int getFromCompartmentIndex() {
+            return fromCompartmentIndex;
+        }
+        
+        public int getToCompartmentIndex() {
+            return toCompartmentIndex;
+        }
+        
+        public int getGeneration() {
+            return generation;
+        }
+        
+        public int getAmountToTransfer() {
+            return amountToTransfer;
+        }
+
+        public int compareTo(TransferEvent event) {
+            return Integer.compare(this.generation, event.generation);
+        }
+    }
+}
diff --git a/src/santa/simulator/compartments/Transfer.java b/src/santa/simulator/compartments/Transfer.java
new file mode 100644
index 0000000..f58cca8
--- /dev/null
+++ b/src/santa/simulator/compartments/Transfer.java
@@ -0,0 +1,11 @@
+package santa.simulator.compartments;
+
+import java.util.List;
+
+/**
+ *
+ * @author Bradley R. Jones
+ */
+public interface Transfer {
+    void genomeTransfer(List<Compartment> compartments, int generation, List<CompartmentEpoch> currentEpochs);
+}
diff --git a/src/santa/simulator/compartments/TransferProb.java b/src/santa/simulator/compartments/TransferProb.java
new file mode 100644
index 0000000..560855f
--- /dev/null
+++ b/src/santa/simulator/compartments/TransferProb.java
@@ -0,0 +1,11 @@
+package santa.simulator.compartments;
+
+import santa.simulator.Virus;
+
+/**
+ *
+ * @author Bradley R. Jones
+ */
+public interface TransferProb {
+    public double getProb(Virus virus, int generation);
+}
\ No newline at end of file
diff --git a/src/santa/simulator/fitness/AbstractSiteFitnessFactor.java b/src/santa/simulator/fitness/AbstractSiteFitnessFactor.java
index 96eca48..2cf99e0 100644
--- a/src/santa/simulator/fitness/AbstractSiteFitnessFactor.java
+++ b/src/santa/simulator/fitness/AbstractSiteFitnessFactor.java
@@ -35,7 +35,7 @@ public double computeLogFitness(byte[] sequence) {
 		if (this.logFitness.length != sequence.length) {
 			logFitness = Double.NEGATIVE_INFINITY;
 		} else {
-			for (int site = 0; site < this.logFitness.length; site++) {
+			for (int site: getSites()) {
 				logFitness += this.logFitness[site][sequence[site]];
 				if (logFitness == Double.NEGATIVE_INFINITY) {
 					break;
@@ -59,6 +59,7 @@ public double getLogFitnessChange(StateChange change) {
 		double fit = 0;	 // neutral fitness
 		double[] logFitnessPosition = null;
 		try {
+                    if (getSites().contains(change.position))
 			logFitnessPosition = logFitness[change.position];
 		} catch(IndexOutOfBoundsException e) {
 			// catch IndexOutOfBoundsException b/c insertions may have
diff --git a/src/santa/simulator/fitness/BetaDistributedPurifyingFitnessModel.java b/src/santa/simulator/fitness/BetaDistributedPurifyingFitnessModel.java
index 6c0aa59..955e589 100644
--- a/src/santa/simulator/fitness/BetaDistributedPurifyingFitnessModel.java
+++ b/src/santa/simulator/fitness/BetaDistributedPurifyingFitnessModel.java
@@ -7,6 +7,7 @@
 
 import org.apache.commons.math3.exception.OutOfRangeException;
 import org.apache.commons.math3.distribution.BetaDistribution;
+import org.apache.commons.math3.random.RandomGenerator;
 
 /**
  * A distribution of fitness effects motivated by
@@ -25,13 +26,14 @@ public class BetaDistributedPurifyingFitnessModel implements PurifyingFitnessMod
     int alphabetSize;
 
     public BetaDistributedPurifyingFitnessModel(double a, double b, double pLethal, int alphabetSize, int sites) {
-
+        RandomGenerator rng = Random.randomData.getRandomGenerator();
+        
         this.alphabetSize = alphabetSize;
         this.pLethal = pLethal;
 
         fitnesses = new double[sites][alphabetSize];
 
-        beta = new BetaDistribution(Random.randomData.getRandomGenerator(), a, b);
+        beta = new BetaDistribution(rng, a, b);
         
 
         for (int i = 0; i < sites; i++) {
@@ -40,11 +42,11 @@ public BetaDistributedPurifyingFitnessModel(double a, double b, double pLethal,
             f.add(1.0);
             for (int j = 1; j < alphabetSize; j++) {
 
-                if (Math.random() < pLethal) {
+                if (rng.nextDouble() < pLethal) {
                     f.add(0.0);
                 } else {
                     try {
-						f.add(beta.inverseCumulativeProbability(Math.random()));
+						f.add(beta.inverseCumulativeProbability(rng.nextDouble()));
 					} catch (OutOfRangeException e) {
 						e.printStackTrace();
 					}                    
diff --git a/src/santa/simulator/fitness/NoFitnessFactor.java b/src/santa/simulator/fitness/NoFitnessFactor.java
new file mode 100644
index 0000000..2604cc5
--- /dev/null
+++ b/src/santa/simulator/fitness/NoFitnessFactor.java
@@ -0,0 +1,32 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package santa.simulator.fitness;
+
+import java.util.Set;
+import santa.simulator.genomes.Feature;
+import santa.simulator.genomes.StateChange;
+
+/**
+ *
+ * @author Bradley R. Jones
+ */
+public class NoFitnessFactor extends AbstractFitnessFactor {
+
+    public NoFitnessFactor(Feature feature, Set<Integer> sites) {
+        super(feature, sites);
+    }
+
+    @Override
+    public double computeLogFitness(byte[] states) {
+        return Double.NEGATIVE_INFINITY;
+    }
+
+    @Override
+    public double getLogFitnessChange(StateChange change) {
+        return 0;
+    }
+    
+}
diff --git a/src/santa/simulator/fitness/PurifyingFitnessRank.java b/src/santa/simulator/fitness/PurifyingFitnessRank.java
index 6962db3..2cac47e 100644
--- a/src/santa/simulator/fitness/PurifyingFitnessRank.java
+++ b/src/santa/simulator/fitness/PurifyingFitnessRank.java
@@ -1,7 +1,7 @@
 package santa.simulator.fitness;
 
 import santa.simulator.genomes.*;
-
+import santa.simulator.Random;
 
 import java.util.*;
 
@@ -229,7 +229,7 @@ private List<HistogramEntry> createHistogram(SequenceAlphabet alphabet, boolean
 		}
 
 		if (breakTiesRandomly)
-			Collections.shuffle(counts);
+			Random.shuffle(counts);
 
 		Collections.sort(counts);
 		return counts;
diff --git a/src/santa/simulator/genomes/BaseGenePool.java b/src/santa/simulator/genomes/BaseGenePool.java
index e164d9e..1289bf1 100644
--- a/src/santa/simulator/genomes/BaseGenePool.java
+++ b/src/santa/simulator/genomes/BaseGenePool.java
@@ -12,9 +12,10 @@
 public abstract class BaseGenePool implements GenePool {
     protected int uniqueGenomeCount = 0;
     protected final int[][] stateFrequencies;
-    protected final LinkedList<Genome> genomes = new LinkedList<Genome>();
-    protected final LinkedList<Genome> unusedGenomes = new LinkedList<Genome>();
+    protected final LinkedList<Genome> genomes = new LinkedList<>();
+    protected final LinkedList<Genome> unusedGenomes = new LinkedList<>();
 
+    @Override
     public LinkedList<Genome> getGenomes() {
         return genomes;
     }
@@ -26,6 +27,7 @@ public BaseGenePool() {
         stateFrequencies = new int[GenomeDescription.root.getGenomeLength()][4];
     }
 
+    @Override
     public void initialize() {
         unusedGenomes.clear();
         //unusedGenomes.addAll(genomes);
@@ -34,6 +36,7 @@ public void initialize() {
     }
 
 
+    @Override
 	public Genome createGenome(Sequence sequence, GenomeDescription gd) {
 		Genome newGenome = createGenome(sequence);
 		newGenome.setDescription(gd);
@@ -42,6 +45,7 @@ public Genome createGenome(Sequence sequence, GenomeDescription gd) {
     }
 
 	
+    @Override
     public int[][] getStateFrequencies() {
         calculateStateFrequencies();
         return stateFrequencies;
@@ -71,6 +75,7 @@ private boolean uniformPool() {
 	 * frequencies.
 	 *
 	 **/
+    @Override
     public int[][] getStateFrequencies(Feature feature, Set<Integer> sites) {
         int[][] freqs = new int[sites.size()][feature.getAlphabet().getStateCount()];
 
@@ -110,6 +115,7 @@ public int[][] getStateFrequencies(Feature feature, Set<Integer> sites) {
 	 * meaningful consensus without first aligning the sequences.
 	 **/
 
+    @Override
     public Sequence getConsensusSequence() {
 		/*
 		 * Fail if all genomes do not have the same GenomeDescription.
@@ -154,6 +160,7 @@ private void calculateStateFrequencies() {
         }
     }
 
+    @Override
     public void updateAllFitnesses(FitnessFunction fitnessFunction) {
         for (Genome genome : genomes) {
             fitnessFunction.computeLogFitness(genome);
@@ -166,6 +173,7 @@ public void updateAllFitnesses(FitnessFunction fitnessFunction) {
      * @param genome2 another genome
      * @return the hamming distance
      */
+    @Override
     public int hammingDistance(Genome genome1, Genome genome2) {
         return hammingDistance(genome1.getSequence(), genome2.getSequence());
     }
@@ -180,10 +188,12 @@ public int hammingDistance(Sequence sequence1, Sequence sequence2) {
         return distance;
     }
 
+    @Override
     public int getUniqueGenomeCount() {
         return uniqueGenomeCount;
     }
 
+    @Override
     public int getUnusedGenomeCount() {
         return unusedGenomes.size();
     }
diff --git a/src/santa/simulator/genomes/BaseGenome.java b/src/santa/simulator/genomes/BaseGenome.java
index 2e1584b..cd6a188 100644
--- a/src/santa/simulator/genomes/BaseGenome.java
+++ b/src/santa/simulator/genomes/BaseGenome.java
@@ -16,16 +16,19 @@ public BaseGenome() {
 		this.descriptor = GenomeDescription.root;
 	}
 
+        @Override
 	public void setDescription(GenomeDescription gd) {
 		this.descriptor = gd;
 		assert(this.descriptor.getGenomeLength() == getLength());
 	}
 
 	// REMIND - do we still need this?
+        @Override
 	public GenomeDescription getDescription() {
 		return descriptor;
 	}
 
+        @Override
 	public int getTotalMutationCount() {
 		return totalMutationCount;
 	}
@@ -38,22 +41,27 @@ protected void incrementTotalMutationCount() {
 		totalMutationCount++;
 	}
 
+        @Override
 	public int getFrequency() {
 		return frequency;
 	}
 
+        @Override
 	public void setFrequency(int frequency) {
 		this.frequency = frequency;
 	}
 
+        @Override
 	public void incrementFrequency() {
 		frequency++;
 	}
 
+        @Override
 	public double getLogFitness() {
 		return logFitness;
 	}
 
+        @Override
 	public void setLogFitness(double logFitness) {
 		if (logFitness != this.logFitness) {
 			this.logFitness = logFitness;
@@ -61,6 +69,7 @@ public void setLogFitness(double logFitness) {
 		}
 	}
 
+        @Override
 	public double getFitness() {
 		if (!fitnessKnown) {
 			fitness = Math.exp(logFitness);
@@ -69,10 +78,12 @@ public double getFitness() {
 		return fitness;
 	}
 
+        @Override
 	public FitnessFunction.FitnessGenomeCache getFitnessCache() {
 		return fitnessCache;
 	}
 
+        @Override
 	public void setFitnessCache(FitnessFunction.FitnessGenomeCache fitnessCache) {
 		this.fitnessCache = fitnessCache;
 	}
@@ -82,6 +93,7 @@ public void setFitnessCache(FitnessFunction.FitnessGenomeCache fitnessCache) {
 	 *
 	 * @return byte array of nucleotides (encoded as integer states)
 	 **/
+        @Override
 	public byte[] getNucleotides(Feature feature) {
 		byte[] nucleotides = null;
 		Feature f = descriptor.getFeature(feature.getName());
@@ -99,6 +111,7 @@ public byte[] getNucleotides(Feature feature) {
 	}
 
 
+        @Override
 	public byte[] getStates(Feature feature) {
 		Sequence seq = new SimpleSequence(getNucleotides(feature));
 		return seq.getStates(feature.getAlphabet());
@@ -122,10 +135,11 @@ public byte[] getStates(Feature feature) {
 	 * information.  Other fitness functions ignore the data computed
 	 * here.
 	 *
-	 * @param feature Feature object over which the changes should be computed.
+	 * @param featureByName Feature object over which the changes should be computed.
 	 * @param mutations set of mutations that are inducing changes.
 	 * @return list of <StateChange> objects
 	 **/
+        @Override
 	public List<StateChange> getChanges(Feature featureByName, SortedSet<Mutation> mutations) {
 		List<StateChange> changes = new ArrayList<StateChange>();
 
@@ -226,11 +240,11 @@ public List<StateChange> getChanges(Feature featureByName, SortedSet<Mutation> m
 	}
 
 
+        @Override
 	public int binomialDeviate(double mutationRate) {
 		return descriptor.binomialDeviate(mutationRate);
 	}
 
-
 	/**
 	 * Reference to an GenomeDescription.  It is through the
 	 * decription that one can obtain Feature coordinates and SiteMaps
diff --git a/src/santa/simulator/genomes/CompactGenome.java b/src/santa/simulator/genomes/CompactGenome.java
index 6d0a216..db361ee 100644
--- a/src/santa/simulator/genomes/CompactGenome.java
+++ b/src/santa/simulator/genomes/CompactGenome.java
@@ -174,4 +174,12 @@ static void setMasterSequence(Sequence masterSequence) {
 
     private static Sequence masterSequence = null;
     
+    @Override
+    public Genome copy() {
+        CompactGenome g = new CompactGenome();
+        
+        g.duplicate(this);
+
+        return g;
+    }
 }
diff --git a/src/santa/simulator/genomes/Genome.java b/src/santa/simulator/genomes/Genome.java
index 9810f5b..1e98bb9 100644
--- a/src/santa/simulator/genomes/Genome.java
+++ b/src/santa/simulator/genomes/Genome.java
@@ -56,5 +56,7 @@ public interface Genome {
 
 	GenomeDescription getDescription();
 	void setDescription(GenomeDescription gd);
+        
+    Genome copy();
 
 }
diff --git a/src/santa/simulator/genomes/SimpleGenome.java b/src/santa/simulator/genomes/SimpleGenome.java
index 02ad2f6..792d235 100644
--- a/src/santa/simulator/genomes/SimpleGenome.java
+++ b/src/santa/simulator/genomes/SimpleGenome.java
@@ -11,7 +11,7 @@ public SimpleGenome() {
 
 	public void duplicate(SimpleGenome source) {
 		this.sequence = new SimpleSequence(source.sequence);
-		this.fitnessCache = source.fitnessCache.clone();
+                this.fitnessCache = source.fitnessCache.clone();
 		this.descriptor = source.descriptor;
 		setLogFitness(source.getLogFitness());
 		assert(this.descriptor.getGenomeLength() == this.sequence.getLength());
@@ -134,6 +134,14 @@ public boolean delete(int position, int count) {
 	public boolean insert(int position, SimpleSequence seq) {
 		return sequence.insertSequence(position, seq);
 	}
+        
+        public Genome copy() {
+            SimpleGenome g = new SimpleGenome();
+            
+            g.duplicate(this);
+            
+            return g;
+        }
 
 	// private members
 
diff --git a/src/santa/simulator/mutators/AbstractMutator.java b/src/santa/simulator/mutators/AbstractMutator.java
index 756fc6d..64fb292 100644
--- a/src/santa/simulator/mutators/AbstractMutator.java
+++ b/src/santa/simulator/mutators/AbstractMutator.java
@@ -23,7 +23,10 @@ public SortedSet<Mutation> mutate(Genome genome) {
         // iterate. This would avoid the sort at the end.
         SortedSet<Mutation> mutations = new TreeSet<Mutation>();
         
-        int mutationCount = genome.binomialDeviate(mutationRate);
+        int mutationCount = 0;
+        
+        if (mutationRate > 0)
+            mutationCount = genome.binomialDeviate(mutationRate);
 
         // We expect only a few mutations per genome. Therefore, simply check
         // by looping over the already generated mutations to avoid duplicates hits.
diff --git a/src/santa/simulator/replicators/RecombinantReplicator.java b/src/santa/simulator/replicators/RecombinantReplicator.java
index b253a53..ff78f7e 100644
--- a/src/santa/simulator/replicators/RecombinantReplicator.java
+++ b/src/santa/simulator/replicators/RecombinantReplicator.java
@@ -1,7 +1,6 @@
 package santa.simulator.replicators;
 
 import java.util.Arrays;
-import java.util.Comparator;
 import java.util.SortedSet;
 import java.util.TreeSet;
 import java.util.List;
diff --git a/src/santa/simulator/samplers/AlignmentSampler.java b/src/santa/simulator/samplers/AlignmentSampler.java
index 237ce2d..f21b677 100644
--- a/src/santa/simulator/samplers/AlignmentSampler.java
+++ b/src/santa/simulator/samplers/AlignmentSampler.java
@@ -44,7 +44,7 @@ public enum Format {
      * @param consensus   write the consensus sequence of the sample rather than writing the sample ?
      * @param schedule    amount of sequences to sample at irregular intervals
      * @param format      format
-     * @param label       label with possible %g, %s, %t, and %f variables
+     * @param label       label with possible %g, %s, %r, %a, %c and %f variables
      * @param fileName    name of the file to write the samples
      */
     public AlignmentSampler(Feature feature, Set<Integer> sites, int sampleSize, boolean consensus,
@@ -69,7 +69,7 @@ public AlignmentSampler(Feature feature, Set<Integer> sites, int sampleSize, boo
     public void initialize(int replicate) {
 
         this.replicate = replicate;
-        String fName = substituteVariables(fileName, 0, 0, 0.0);
+        String fName = substituteVariables(fileName, 0, 0, null, 0.0);
 
         try {
             destination = new PrintStream(fName);
@@ -96,11 +96,25 @@ public void initialize(int replicate) {
         }
     }
 
-    private String substituteVariables(String name, int generation, int seq, double fitness) {
+    private String substituteVariables(String name, int generation, int seq, Virus virus, double fitness) {
         String result = name.replaceAll("%r", String.valueOf(replicate+1));
         result = result.replaceAll("%g", String.valueOf(generation));
         result = result.replaceAll("%s", String.valueOf(seq));
         result = result.replaceAll("%f", String.valueOf(fitness));
+        
+        if (virus != null) {
+            // generation when lineage entered its compartment
+            result = result.replaceAll("%a", String.valueOf(virus.getAge()));
+            
+            // track last compartment
+            if (virus.getLastCompartment() != null) {
+                result = result.replace("%c", virus.getLastCompartment().getName());
+            }
+        }
+        
+        result = result.replaceAll("%a", "NA");
+        result = result.replaceAll("%c", "NA");
+        
         return result;
     }
 
@@ -166,14 +180,14 @@ protected Virus[] getSample(int generation, Population population) {
 
     private void writeNexusFormat(int generation, Virus[] sample) {
         if (consensus) {
-            String l = substituteVariables(label, generation, 0, 0.0);
+            String l = substituteVariables(label, generation, 0, null, 0.0);
 
             destination.print(l + "\t");
             destination.println(computeConsensus(sample));
         } else {
             int i = 1;
             for (Virus virus : sample) {
-                String l = substituteVariables(label, generation, i, virus.getFitness());
+                String l = substituteVariables(label, generation, i, virus, virus.getFitness());
 
                 destination.print(l + "\t");
 
@@ -231,7 +245,7 @@ private String computeConsensus(Virus[] sample) {
 
     private void writeFastaFormat(int generation, Virus[] sample) {
         if (consensus) {
-            String l = substituteVariables(label, generation, 0, 0.0);
+            String l = substituteVariables(label, generation, 0, null, 0.0);
 
             destination.println(">" + l);
             destination.println(computeConsensus(sample));
@@ -239,7 +253,7 @@ private void writeFastaFormat(int generation, Virus[] sample) {
             int i = 1;
 
             for (Virus virus : sample) {
-                String l = substituteVariables(label, generation, i, virus.getFitness());
+                String l = substituteVariables(label, generation, i, virus, virus.getFitness());
 
                 destination.println(">" + l);
                 destination.println(virus.getGenome().getSequence().getNucleotides());
@@ -255,7 +269,7 @@ private void writeXMLFormat(int generation, Virus[] sample) {
         destination.println("<!-- Generation = " + generation + " -->");
         int i = 1;
         for (Virus virus : sample) {
-            String l = substituteVariables(label, generation, i, virus.getFitness());
+            String l = substituteVariables(label, generation, i, virus, virus.getFitness());
             destination.println("\t<sequence label=\"" + l+ "\">");
             destination.println("\t\t" + virus.getGenome().getSequence().getNucleotides());
             destination.println("\t</sequence>");
diff --git a/src/santa/simulator/selectors/ClonalExpansionSelector.java b/src/santa/simulator/selectors/ClonalExpansionSelector.java
new file mode 100644
index 0000000..d45f833
--- /dev/null
+++ b/src/santa/simulator/selectors/ClonalExpansionSelector.java
@@ -0,0 +1,43 @@
+package santa.simulator.selectors;
+
+import java.util.Collections;
+import java.util.List;
+import santa.simulator.Random;
+import santa.simulator.Virus;
+
+/**
+ *
+ * @author Bradley R. Jones
+ */
+public class ClonalExpansionSelector implements Selector {
+    private double splitProbability;
+    private double deathProbability;
+    private double persistProbability;
+    
+    public ClonalExpansionSelector(double splitProbability, double deathProbability) {
+        this.splitProbability = splitProbability;
+        this.deathProbability = deathProbability;
+        this.persistProbability = 1 - deathProbability;
+    }
+
+    public void selectParents(List<Virus> currentGeneration, List<Integer> selectedParents, int sampleSize) {
+        for(int i = 0; i < currentGeneration.size(); ++i) {
+            double fitness = currentGeneration.get(i).getFitness();
+            int nbChildren = 0;
+            
+            double draw = Random.nextUniform(0, 1);
+            if (draw < persistProbability * fitness) {
+                if (draw < splitProbability * fitness) {
+                    nbChildren = 2;
+                } else {
+                    nbChildren = 1;
+                }
+            }
+            
+            for(long n = 0; n < nbChildren * sampleSize; ++n) {
+                selectedParents.add(i);
+            }
+        }
+        Random.shuffle(selectedParents);
+    }
+}
diff --git a/src/santa/simulator/selectors/DynamicSelector.java b/src/santa/simulator/selectors/DynamicSelector.java
index 7647e54..a4ec651 100644
--- a/src/santa/simulator/selectors/DynamicSelector.java
+++ b/src/santa/simulator/selectors/DynamicSelector.java
@@ -1,6 +1,5 @@
 package santa.simulator.selectors;
 
-import java.util.Collections;
 import java.util.List;
 
 import santa.simulator.Random;
@@ -24,20 +23,27 @@ public DynamicSelector(double growthRate, double carryingPopulation) {
 		this.carryingPopulation = carryingPopulation;
 	}
 
+        @Override
 	public void selectParents(List<Virus> currentGeneration, List<Integer> selectedParents, int nbOfParents) {
+            Random.shuffle(currentGeneration);
 		for(int i = 0; i < currentGeneration.size(); ++i) {
 			double fitness = currentGeneration.get(i).getFitness();
-			//Abbas: The below formulation of logistic growth was implemented by Gertjan
+                        
+                        //Abbas: The below formulation of logistic growth was implemented by Gertjan
 			//It was noticed that for slower growth rates, the simulator overshoots the carrying size.
 			//A slightly different formulation is introduced according to: https://www.maa.org/press/periodicals/loci/joma/logistic-growth-model-background-logistic-modeling
 			//expectedProgenyCount =  Math.max(fitness * (1 + growthRate*(1-selectedParents.size()/carryingPopulation)),Double.MIN_VALUE);
-			expectedProgenyCount =  Math.max(fitness * growthRate*(1-selectedParents.size()/carryingPopulation),Double.MIN_VALUE);
-			long nbChildren = fitness == 0 ? 0 : Random.nextPoisson(expectedProgenyCount);
+			expectedProgenyCount =  fitness * growthRate * (1 - selectedParents.size() / carryingPopulation);
+                        
+                        // Set to zero if infinite fitness is observed (this usually happens if zero fitness is changed to nonzero fitness)
+			long nbChildren = 0;
+                        if (fitness > 0 && Double.isFinite(fitness) && expectedProgenyCount > Double.MIN_VALUE)
+                                nbChildren =  Random.nextPoisson(expectedProgenyCount);
 			for(long n = 0; n < nbChildren * nbOfParents; ++n) {
 				selectedParents.add(i);
 			}
 		}
-		Collections.shuffle(selectedParents);
+		Random.shuffle(selectedParents);
 	}
 
 }
diff --git a/src/santa/simulator/selectors/RouletteWheelSelector.java b/src/santa/simulator/selectors/RouletteWheelSelector.java
index 5633313..c34148e 100644
--- a/src/santa/simulator/selectors/RouletteWheelSelector.java
+++ b/src/santa/simulator/selectors/RouletteWheelSelector.java
@@ -35,7 +35,7 @@ public void selectParents(List<Virus> currentGeneration, List<Integer> selectedP
 			i++;
 		} while (i < populationSize);
 
-		Collections.shuffle(selectedParents);
+		Random.shuffle(selectedParents);
 	}
 
 	private final void calculateCumulativeFitness(List<Virus> currentGeneration) {
diff --git a/test/santa/simulator/RandomTest.java b/test/santa/simulator/RandomTest.java
new file mode 100644
index 0000000..615a9c0
--- /dev/null
+++ b/test/santa/simulator/RandomTest.java
@@ -0,0 +1,67 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package santa.simulator;
+
+import java.util.ArrayList;
+import java.io.FileWriter;
+
+/**
+ *
+ * @author Bradley R. Jones
+ */
+public class RandomTest {
+    
+    private static final long SEED = 1989;
+    
+    public RandomTest() {
+    }
+    
+    // Not a real test
+    public ArrayList<Long> generatePoissons() {
+        Random.setSeed(SEED);
+        
+        final long count = 1000;
+        final double mean1 = 1.0;
+        final double mean2 = 100000.0;
+        final double mean3 = 0.1;
+        
+        ArrayList<Long> list = new ArrayList<Long>();
+        
+        System.out.println("Mean: " + mean1);
+        for (long i = 0; i < count; i++)  
+            list.add(Random.nextPoisson(mean1));
+        System.out.println("Mean: " + mean2);
+        for (long i = 0; i < count; i++)
+            list.add(Random.nextPoisson(mean2));
+        System.out.println("Mean: " + mean3);
+        for (long i = 0; i < count; i++)
+            list.add(Random.nextPoisson(mean3));
+        
+        return list;
+    }
+    
+    public static void main(String[] args) {
+        try {
+            if (args.length > 0) {
+                String filename = args[0];                
+                FileWriter writer = new FileWriter(filename);
+                
+                RandomTest test = new RandomTest();
+                ArrayList<Long> poissons = test.generatePoissons();
+                
+                for (long value: poissons) {
+                    writer.write("" + value + "\n");
+                }
+                
+                writer.close();
+            } else {
+                throw new Exception("Need to specify output filename.");
+            }
+        } catch (Exception e) {
+            System.out.println(e.getMessage());
+        }
+    }
+}