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Update ColorByClade.py

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Changed to root on bacteria (Ba) and not prokaryotes (Ba, Za).... did not test
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Katzlab 2025-07-01 16:18:54 -04:00 committed by GitHub
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Utilities/for_trees/ColorByClade.py
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@ -151,7 +151,7 @@ def reroot(tree):
return best_clade return best_clade
#Get the biggest clade for each taxonomic group (stops once it finds one) #Get the biggest clade for each taxonomic group (stops once it finds one)
for taxon in [('Ba', 'Za'), ('Op'), ('Pl'), ('Am'), ('Ex'), ('Sr')]: for taxon in [('Ba'), ('Za'), ('Op'), ('Pl'), ('Am'), ('Ex'), ('Sr')]:
clade = get_best_clade(taxon) clade = get_best_clade(taxon)
if len([leaf for leaf in clade if leaf.name[:2] in taxon]) > 3: if len([leaf for leaf in clade if leaf.name[:2] in taxon]) > 3: