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Unrooted tree is used to run AdaptML. Usually I make them with phyml for 2,000 or fewer sequences:
/home/digev/Softs/phyml_v2.4.4/exe/phyml_linux all_u.phy 0 i 1 100 GTR e e 4 e BIONJ y y
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Once you have found a set of stable habitats you want to go with, then make the clusters. This example is for the tree ./example_noroot.phy_phyml_tree.txt3, outgroup ECK_1 using 9900.file to make the final clusters :/home/software/python/python-(using python 2.5.1 and you may have to change the paths to point to the AdaptML software):
/bin/python ~/AdaptML_dir/latest_AdaptML/habitats/trunk/AdaptML_Analyze.py tree=./example_noroot.phy_phyml_tree.txt3 hab0=16 outgroup=ECK_1 write=./example_dir thresh=0.05
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mkdir ./example_dir/rand_trials
/home/software/python/python-2.5.1/bin/python ~/AdaptML_dir/latest_AdaptML/clusters/getstats/rand_JointML.py habitats=./example_dir/migration.matrix mu=./example_dir/mu.val tree=./example_noroot.phy_phyml_tree.txt3 outgroup=ECK_1 write=./example_dir/rand_trials/
/home/software/python /python-2.5.1/bin/python ~/AdaptML_dir/latest_AdaptML/clusters/getstats/GetLikelihoods.py ./example_dir/rand_trials/ ./example_dir/
/home/software/python/python-2.5.1/bin/python ~/AdaptML_dir/latest_AdaptML/clusters/trunk/JointML.py habitats=./example_dir/migration.matrix mu=./example_dir/mu.val color=./example_dir/color.file tree=./example_noroot.phy_phyml_tree.txt3 write=./example_dir/ outgroup=ECK_1 thresh=./example_dir/9900.file
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