[phylocom-user] phylomatic troubleshooting

Cam Webb cwebb at oeb.harvard.edu
Wed Dec 14 20:27:17 PST 2011


Dear Rachel,

There are no internal node names in your tree file (i.e. a genus name at 
the base of the clade of congeners), so the program cannot hook in your 
new taxa.  Please see the attached as a demonstration. I added a name to 
the Astragalus clade root and the Trifolium clade root, and edited the 
taxa file to just include Astragalus and Trifolium taxa.

Best,

Cam


On Wed, 14 Dec 2011, Rachel Prunier wrote:

> Hello - 
> I am having a vexing problem with phylomatic, and I am hoping someone might
> be able to help me.  When I input my tree file and taxa file (attached
> below) phylomatic runs, but the resulting tree does not have any internal
> structure (i.e. it is a big polytomy except where I indicated relationships
> in the taxa file.  
> 
> I suspect that there is something subtly wrong with the formatting of my
> tree file.  The taxa file, when run with a different tree file (which
> differs in a few ways, one of which is that it doesn't have branch lengths),
> produces a tree with the proper internal structure.  
> 
> These are the steps that I have taken to make my tree file is properly
> formatted:
> 1.  collapsed small branch lengths into polytomies, and ensured that there
> is no scientific notation in the tree (di2multi in R)
> 2.  rooted the tree with the outgroup (root in R)
> 
> Thanks in advance!
> 
> Rachel
> 
> 
> Rachel Prunier, PhD.
> Assistant Director for Education and
> Research Associate
> Kellogg Biological Station
> 3700 East Gull Lake Drive
> Hickory Corners, MI 49060
> prunier at msu.edu
> (269) 671- 2350
> 
> ***********************************************
> 
> "An inconvenience is only an adventure wrongly considered."
> G. K. Chesterton
> 
> 
> 
> 
> 
>
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(((Astragalus_crassicarpus:0.356404,Astragalus_missouriensis:0.356404,Astragalus_nuttallianus:0.356404)Astragalus:0.072234,(Trifolium_campestre:0.353963,(Trifolium_pratense:0.235976,(Trifolium_dasyphyllum:0.157317,Trifolium_hybridum:0.157317)Vestriin:0.078659)Trifoliuma:0.117988,Trifolium_repens:0.057798)Trifolium:0.074674):0.311964);
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