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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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.eduwrote:

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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galaxy-user@lists.bx.psu.edu

http://lists.bx.psu.edu/listinfo/galaxy-user

-- 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

Hi melissa,

Your tree definition is alright. HYPHY is throwing an internal error, which is possibly due to large lengths of your sequences. I'll email Sergei about the same and see what he has to say.

Thanks, Guru.

On Sep 7, 2010, at 2:58 PM, Melissa A. Wilson Sayres wrote:

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

---

galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

-- 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