# Phylogenetic tree commands

**URL:** <https://forum.mothur.org/t/phylogenetic-tree-commands/1482>\
**Category:** Commands in mothur\
**Created:** [August 30, 2013, 12:14am UTC](https://forum.mothur.org/t/phylogenetic-tree-commands/1482 "2013-08-30T00:14:09Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Fab](https://avatars.discourse-cdn.com/v4/letter/f/51bf81/32.png) [@Fab](https://forum.mothur.org/u/Fab)\
**Post date:** [August 30, 2013, 12:14am UTC](https://forum.mothur.org/t/phylogenetic-tree-commands/1482/1 "2013-08-30T00:14:09Z")

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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

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**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [September 3, 2013, 11:59am UTC](https://forum.mothur.org/t/phylogenetic-tree-commands/1482/2 "2013-09-03T11:59:06Z")

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

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**Author:** ![Fab](https://avatars.discourse-cdn.com/v4/letter/f/51bf81/32.png) [@Fab](https://forum.mothur.org/u/Fab)\
**Post date:** [September 4, 2013, 4:13pm UTC](https://forum.mothur.org/t/phylogenetic-tree-commands/1482/3 "2013-09-04T16:13:28Z")

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Thanks, Pat.

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

![](http://i42.tinypic.com/wrz8tf.png)