I’m trying to make a tree file with clearcut and there is no option to group my sequences except with a group or a name file, which, to my understanding, have been replaced with count files. Is there a way to get a count file in classify.tree to specify what sequences belong to which group?
For clearcut, the only file you can give it is a phylip-formatted distance matrix. For things like phylo diversity and the unifracs, you can provide a count file along with the tree file and design to indicate what sequences go with what samples/groupings
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