Version 3.1.1.MF2

• Updated multi-threading strategy for ModelFinder, PartitionFinder, and Tree Search.
• Clean up the output of ModelFinder according to: iqtree/iqtree2#14

Version 3.1.1.CMIX

• Codon Mixture Models: M1a, M2a, M3, M7 and M8
• SBA feature
• Flexible syntax for parameter specification

Version 3.0.1.1

• Updated version of mixture finder
• The issue of checkpoint inconsistency has been fixed
• An option -writefreqchkpt is introduced to force writing out nucl/aa freqs to the checkpoint files
• An option -mfopt is introduced for further optimising the nucl/aa frequencies in the mixture model.

Version 2.4.2

The version allows --model-joint to support mixture with predefined frequencies. The model was suggested by Ryo.
For example:

iqtree3 -S best_model.nex -te treefile.txt --model-joint "MIX{LG+FC10pi1,LG+FC10pi2,WAG+FC10pi3,WAG+FC10pi4,Q.pfam+FC10pi5,Q.pfam+FC10pi6}"

Version 2.4.1

An option is added to adjust the FunDi model's epsilon value. This version has been sent to Andrew's group for testing.