On Tue, Sep 7, 2010 at 4:28 PM, Guruprasad Ananda <gua110@bx.psu.edu> wrote:

Hi Melissa,

So looks like you'll have to use 'N' as a masking character instead of #. You can either rerun quality masking on your alignments or do the following to convert your #s to Ns in your masked fasta files.

1. Convert fasta to tabular
2. Use 'Text manipulation -> Compute' tool on the tabular file from step(1) to convert #s to Ns, using the following expression: c2.replace(chr(35),"N")

3. Convert output of step(2) to Fasta using 'Convert formats -> Tabular-to-FASTA' tool with c1 as title column and c3 as sequence column.

Thanks,
Guru.

Begin forwarded message:

From: Guruprasad Ananda <gua110@bx.psu.edu>

Date: September 7, 2010 4:07:54 PM EDT

To: Sergei L Kosakovsky Pond <spond@ucsd.edu>

Cc: "Melissa A. Wilson Sayres" <mwilsonsayres@gmail.com>, Galaxy Lab <galaxy-lab@bx.psu.edu>

Subject: Re: [galaxy-lab] Question about Branch Lengths Estimation

Thanks Sergei! Melissa's alignments have been masked by quality scores. Will it work if she used N as a masking character instead of #?

Guru.

On Sep 7, 2010, at 4:04 PM, Sergei L Kosakovsky Pond wrote:

Hi Guru,

The alignment you attached contains '#' inside sequence strings.
HyPhy will skip those, creating misaligned sequences of differing lengths.
The error you see happens if the first sequence is shorter than others.

There are two solutions:

1). Replace '#' with characters that HyPhy understands (e.g. '-')

2). Tell HyPhy to accept '#' as a valid token.
I think this option can only work with NEXUS input files, because '#' is a sequence delimiter in the MEGA format, which HyPhy tries to autodetect...

Sergei

Hi Sergei,

Melissa is trying to use HYPHY branch lengths estimator on Galaxy on 4-way primate alignments. HYPHY is however producing the following error:

Error:
Internal Error in '
Write2Site' - index is too high (using compact representation)

Call stack
2 : Read Data Set ds from file PROMPT_FOR_FILE
1 : ExecuteAFile from file "/tmp/tmpX5jYY7" using basepath /tmp/. reading input from _genomeScreenOptions

Is this because her sequence lengths are pretty big? Is there a limi on sequence lengths?

Here is a sample input file that causes this problem, in case you wanted a test case:
http://bx.psu.edu/~gua110/Galaxy165-%5bchr22_HCOM_fasta%5d.fasta
Tree = ((hg18,panTro2),ponAbe2),rheMac2)

Thanks,

Guru.

Begin forwarded message:

From: "Melissa A. Wilson Sayres" <mwilsonsayres@gmail.com>

Date: September 7, 2010 2:58:44 PM EDT
To: Guruprasad Ananda <gua110@bx.psu.edu>

Cc: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>

Subject: Re: Question about Branch Lengths Estimation

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

/-------------------------------------------------------------------------------------------------/

Ignorance more frequently begets confidence than does knowledge

Charles Darwin

/-------------------------------------------------------------------------------------------------/

Sergei L. Kosakovsky Pond, Ph.D.

Assistant Adjunct Professor
Division of Infectious Diseases

Division of Biomedical Informatics
School of Medicine
University of California San Diego

Theodore Gildred Facitlity
220 Dickinson St Suite A
San Diego, CA 92103
USA

Phone: +1 619 543 8898
Fax : +1 619 543 5066
Web : http://www.hyphy.org/sergei/

HyPhy Page: http://www.hyphy.org/
Adaptive Evolution Server: http://www.datamonkey.org/

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