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The original migration.tab file in ./040609_dir/ has 6 habitats, so just use that to see the percent matching.
Then use get_stable_habitats5habitats6.pl and you might have to change the percent matching
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foreach? /home/software/python/python-2.5.1/bin/python ~/AdaptML_dir/latest_AdaptML/habitats/trunk/AdaptML_Analyze.py tree=./${f}_noroot.phy_phyml_tree.txt3 hab0=16 outgroup=ECK_1 write=./${f}_dir thresh=0.05
foreach? perl ~/bin/migration2color_codes.pl ./${f}_dir/migration.matrix ~/bin/color_template.txt > ./${f}_dir/color.file
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