I have created a tree file with the extension .tre using the dist.seqs and clearcut commands. I have looked at my file in Figtree. It has a representative sequence name identifying each leaf. What do I need to do in order to have each leaf display the organism name?
So mothur really isn’t designed to be a phylogenetics package. For this type of analysis, you’d probably be best served using something like ARB. For a quick fix, you could always change the names in the tre file.