Question About Branch Lengths Estimation

Question: Question About Branch Lengths Estimation

8.2 years ago by

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 <http: main.g2.bx.psu.edu="" history=""> 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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modified 8.2 years ago by Guruprasad Ananda • 230 • written 8.2 years ago by Melissa A. Wilson Sayres • 60

8.2 years ago by

Guruprasad Ananda • 230

Guruprasad Ananda • 230 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.

ADD COMMENT • link written 8.2 years ago by Guruprasad Ananda • 230

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 -- 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

ADD REPLY • link written 8.2 years ago by Melissa A. Wilson Sayres • 60

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.

ADD REPLY • link written 8.2 years ago by Guruprasad Ananda • 230

Thanks Guru!! It seems I just have a knack for finding these little quirks. :) I really appreciate you figuring this out! Best, 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

ADD REPLY • link written 8.2 years ago by Melissa A. Wilson Sayres • 60

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 < -- 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

ADD REPLY • link written 8.2 years ago by Melissa A. Wilson Sayres • 60

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.

ADD REPLY • link written 8.2 years ago by Guruprasad Ananda • 230

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