...
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:
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