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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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foreach? python ../../latest_adaptml/habitats/trunk/AdaptML_Analyze.py tree=./All_simple_7_ur_particle.phy_phyml_tree.txt2 hab0=16 outgroup=ECK_1 write=./${f}${d}_dir/ thresh=0.025
foreach? perl parse_migration3.pl ./${f}${d}_dir/habitat.matrix > ./${f}${d}_dir/habitat.matrix.tab
foreach? end
Make a list of all of the migration.tab files
ls *_dir/migrationhabitat.matrix.tab > migration_list.txt2
Then use temp_dist2.pl to get the habitat number distribution.
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Once you have found a set of stable habitats you want to go with, then make the clusters (this is another set of commands, could be an old format, I might also be using habitats with 2, 3, 4 and 5 predicted habitats):
foreach f (All_simple_u_4 All_simple_u_3 All_simple_u_5 All_simple_u_2)
. This example is for the tree ./example_noroot.phy_phyml_tree.txt3, outgroup ECK_1 using 9900.file to make the final clusters (using python 2.5.1 and you may have to change the paths to point to the AdaptML software):
foreach? /home/software/python/python-2.5.1/bin/python ~/AdaptML_dir/latest_AdaptML/habitats/trunk/AdaptML_Analyze.py tree=./${f}example_noroot.phy_phyml_tree.txt3 hab0=16 outgroup=ECK_1 write=./${f}example_dir thresh=0.05
foreach? perl ~/bin/migration2color_codes.pl ./${f}example_dir/migration.matrix ~/bin/ color_template.txt > ./${f}example_dir/color.file
foreach? mkdir ./${f}example_dir/rand_trials
foreach? /home/software/python /python-2.5.1/bin/python ~/AdaptML_dir/latest_AdaptML/clusters/getstats/rand_JointML.py habitats=./${f}example_dir/migration.matrix mu=./${f}example_dir/mu.val tree=./${f}example_noroot.phy_phyml_tree.txt3 outgroup=ECK_1 write=./${f}example_dir/rand_trials/
foreach? /home/software/python /python-2.5.1/bin/python ~/AdaptML_dir/latest_AdaptML/clusters/getstats/GetLikelihoods.py ./${f}example_dir/rand_trials/ ./${f}example_dir/
foreach? /home/software/python/python-2.5.1/bin/python ~/AdaptML_dir/latest_AdaptML/clusters/trunk/JointML.py habitats=./${f}example_dir/migration.matrix mu=./${f}example_dir/mu.val color=./${f}example_dir/color.file tree=./${f}example_noroot.phy_phyml_tree.txt3 write=./${f}example_dir/ outgroup=ECK_1 thresh=./${f}example_dir/9900.fileforeach? end