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iqtree / iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
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MixtureFinder #326

Closed josephhughes closed 1 week ago

josephhughes commented 2 weeks ago

I'm running "IQ-TREE multicore version 2.3.6 for Linux x86 64-bit built Aug 1 2024" with the following command: /software/iqtree-v2.3.6/bin/iqtree2 -s test_aa.fa -m MIX+MF --prefix test

following the documentation here: http://www.iqtree.org/doc/Complex-Models

MixtureFinder is an approach to select the optimum number of classes and the substitution model in each class for a mixture model of Q matrices. Starting with version 2.3.1, MixtureFinder is available in IQ-TREE. To run MixtureFinder:

iqtree -s example.phy -m MIX+MF

but I'm getting the following error message:

WARNING: Command-line argument MIX+MF differs from checkpoint MIX WARNING: Command-line differs from checkpoint!

For your convenience alignment with unique sequences printed to test.uniqueseq.phy ERROR: Error! The option -m '' can only work on DNA data set

Is it really only possible to test mixture models for DNA alignments?

roblanf commented 1 week ago

Hi @josephhughes,

MixtureFinder only works with DNA models. This is explained in the paper: https://www.biorxiv.org/content/10.1101/2024.03.20.586035v2

There are lots of mixture models for Amino acids too, these are also available in IQ-TREE and explained in the docs under "Protein mixture models" here: http://www.iqtree.org/doc/Substitution-Models

Rob