Hi Guru,

It worked with most of the HC-files (just one failed: chr1_HC_fasta), but hasn't worked with any of the four-way alignments, using either of these trees:

(((hg18,panTro2),ponAbe2),rheMac2)

nor

((((hg18),panTro2),ponAbe2),rheMac2)

I tested chr1 and chr2.

Ideas?

Thanks!

Melissa

On Tue, Sep 7, 2010 at 1:27 PM, Melissa A. Wilson Sayres <mwilsonsayres@gmail.com> wrote:

Thanks Guru!! 

It seems I just have a knack for finding these little quirks. :)

I really appreciate you figuring this out!

Best,

Melissa

On Tue, Sep 7, 2010 at 11:48 AM, Guruprasad Ananda <gua110@bx.psu.edu> wrote:

Hi Melissa,

This seems to be the case with pairwise alignments only. 3-way and above work well with the regular Newick tree definitions. For instance, for a 4-way alignment, you could use: ((hg17,panTro1),(mm5,rn3))

I'll update the tool help with this info.

Thanks,

Guru.

On Sep 7, 2010, at 11:40 AM, Melissa A. Wilson Sayres wrote:

Hi Guru,

Thanks for getting back to me so quickly!

I'll give that a try and let you know how it goes. If this is the
problem, perhaps the instructions could be updated under the took
because the current directions give a different formatting of the
tree. It is a little counter- intuitive to have to put parentheses
around one species. Do you think it will be the same for four species?
(That I put parentheses around just hg18)

Thanks again!!

Best,
Melissa


On Tuesday, September 7, 2010, Guruprasad Ananda <gua110@bx.psu.edu> wrote:

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:

143: Branch Lengths on data 120

empty, format: tabular, database:hg18Info: 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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--
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

--

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

--
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