Hi Melissa,

Looks like Hyphy doesn't like the way you specified your phylogenetic tree. I tried running the tool on your test dataset with the tree defined as ((hg18),panTro2) and it ran just fine! Please give it a shot and let me know if the problem persists.
You can find a working example of the same here:
http://main.g2.bx.psu.edu/u/guru/h/imported-melissa-test-history  (see history item #8)

Thanks,
Guru.

On Sep 3, 2010, at 5:21 PM, Melissa A. Wilson Sayres wrote:

Hi there,

I am trying to use the tool Branch Lengths Estimation under the Evolution heading.

I have a pairwise alignment - (hg18,panTro2), but when I try to run the tool, using the HKY85 model on my FASTA formatted alignment, I get nothing in the output. 

It doesn't give an error, but instead gives:

empty, format: tabular, database:hg18
Info: Single Alignment Analyses

Any ideas?

Thanks!!
Melissa
--
Melissa A. Wilson Sayres
NSF Graduate Research Fellow, Bioinformatics & Genomics
306 Wartik Lab
University Park, PA 16802
maw397@psu.edu

It is far better to grasp the Universe as it really is than to persist in delusion, however satisfying and reassuring. -- Carl Sagan

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