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Add multiple compartments / populations and genome transfer #32

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cc7a8d1
added Compartments; reworked xml structure a bit
brj1 Mar 23, 2018
7c501f2
added noFitness fitness factor
brj1 Mar 23, 2018
686f812
removed NoFitessFactor; added exponential and logitstic populatins toXML
brj1 Mar 23, 2018
b16adfa
fixed introduced bug
brj1 Mar 23, 2018
ee51fd0
fixed authors
brj1 Mar 26, 2018
501c106
fixed authors
brj1 Mar 26, 2018
9d73930
fixed Virus/Genome transfer
brj1 Mar 27, 2018
1c9d50f
updates
brj1 Mar 27, 2018
e1df7a4
readd
brj1 Mar 23, 2018
604f8fe
fixed Genome copy bug
brj1 Mar 28, 2018
3bf92f0
fixed bugs
brj1 Mar 28, 2018
ac66840
updated HIV-latent.xml
brj1 Apr 12, 2018
6b19c12
merged
brj1 Apr 13, 2018
60597ac
merged and built
brj1 Apr 13, 2018
2e21958
added clonal expansion
brj1 Apr 23, 2018
0344975
added clonalexapansiongrowth
brj1 Apr 24, 2018
02b00cf
Merge branch 'master' into latency
brj1 Apr 24, 2018
b885db1
fixing bugs in virus transfer
brj1 Apr 26, 2018
2b90f87
Merge branch 'latency'
brj1 Apr 26, 2018
5d29507
changed genome transfer to class
brj1 Aug 9, 2018
cd3404e
fixed bugs
brj1 Aug 10, 2018
cf572f8
fixed bugs
brj1 Aug 10, 2018
d68a18d
optimized AbstractSiteFitnessFactor by getting it to only look at the…
brj1 Aug 10, 2018
5cb1575
fixed bug introduced by last change
brj1 Aug 13, 2018
fc5bc63
added recording of compartment tranfers
brj1 Sep 4, 2018
6f81fe5
added citation to fitness
brj1 Sep 12, 2018
eb39e35
reworked transfer to make it modular; aded new exzample files
brj1 Oct 24, 2018
c73331c
small change to latent example
brj1 Dec 3, 2018
6fa5856
fixed bug with low fitnesses calling nextPoission
brj1 Dec 10, 2018
5f97f3b
removed infinity from DynamicSelector; aligned randomness
brj1 Aug 28, 2019
05c3187
add compartment tracking
brj1 Sep 24, 2019
65ec2c4
add and update HIV-1 latent example XMLs
brj1 Dec 17, 2019
f0ec849
updated example XMLs
brj1 Apr 14, 2020
c576aae
changed SimulationEpoch to use List of Epochs instead of matrching by…
Jun 17, 2020
68d983a
Merge remote-tracking branch 'santa-dev/master'
Jun 17, 2020
c683363
added example for within HIV-1 evolution including the latent reservoir
brj1 Nov 3, 2020
dbce312
fix bug where fitness of transferred genomes would be not calculated
brj1 Jan 26, 2023
a5bd594
added varying models from Virus Evol paper
brj1 Aug 23, 2023
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947 changes: 947 additions & 0 deletions examples/HIV-1_latent.xml
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515 changes: 515 additions & 0 deletions examples/HIV_models/HIV-1_C.xml
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947 changes: 947 additions & 0 deletions examples/HIV_models/activegrowth_high.xml
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947 changes: 947 additions & 0 deletions examples/HIV_models/activegrowth_low.xml
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2,114 changes: 2,114 additions & 0 deletions examples/HIV_models/fitness_hla.xml
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237 changes: 237 additions & 0 deletions examples/HIV_models/fitness_none.xml
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<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>
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