[phylocom-user] phylomatic troubleshooting

Rachel Prunier prunier at msu.edu
Wed Dec 14 12:55:11 PST 2011


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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