Phylogenetic tree commands

Commands in mothur
1

Hi All,

Thank you Pat for your great workshop!

I have a question about the tree commands.

When building the tree I use these commands:

mothur > dist.seqs(fasta=final.fasta, output=phylip, processors=2)

mothur > clearcut(phylip=final.phylip.dist)

How can I have Mothur name the different branches with their names instead of the sequences codes assigned from it? Is it looking at the wrong taxonomy file? I use Fig.Tree for visualizing the tree.

Thanks everybody!
Fab

2

You might want to check out http://www.mothur.org/wiki/Classify.tree. That’s the closest thing we’ve got to what you’re describing.

3

Thanks, Pat.

I followed all the directions and commands properly but then this is what I get with the final tree