[Bioperl-l] free software to estimate dS and dN in pairwise comparisons

Wed Jan 11 18:30:52 UTC 2017

Roy's comment was a good one, either way there may be an opportunity to update the algorithms with ones that incorporate tvts rate variation and such.
Mark

On Wed, Jan 11, 2017 at 1:25pm, Fields, Christopher J < cjfields at illinois.edu [cjfields at illinois.edu] > wrote:
Thanks Jason!
I think the idea (which may have been trimmed out in the replies) was to potentially incorporate this into bioperl; I guess the question now is whether this is still necessary.
chris
From: Jason Stajich < jason.stajich at ucr.edu [jason.stajich at ucr.edu] >
Date: Wednesday, January 11, 2017 at 9:52 AM
To: Chris Fields < cjfields at illinois.edu [cjfields at illinois.edu] >
Cc: Carnë Draug < carandraug+dev at gmail.com [carandraug+dev at gmail.com] >, Mark Jensen < maj at fortinbras.us [maj at fortinbras.us] >, bioperl mailing list < bioperl-l at mailman.open-bio.org [bioperl-l at mailman.open-bio.org] >
Subject: Re: [Bioperl-l] free software to estimate dS and dN in pairwise comparisons

Hi - As standalone non-bioperl dependent it seems like it needs it own repo?
Currently we have Ka/Ks calculation in Bio::Align::DNAStatistics - not sure if this implementation is faster?

FYI Carnë - you might also see my fast C implementation pairwise dnds as well that is a hybrid of the yn00 code. https://github.com/hyphaltip/subopt-kaks [https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hyphaltip_subopt-2Dkaks&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=QQfC31p3Me-1RzS8aYNfIE0bYdnUkzAe0wipfYQBuFo&s=cNE_WE8Mb9yxOYR7GgeOsQmaGC4tCz_3qrLrgjF4Zqc&e=]
The main app for already aligned CDS is yn00_cds_prealigned also generates a table of the pairwise values I find this useful for generating fast pairwise e.g. https://github.com/1KFG/analyses/blob/master/Paralog/kaks/Aapi.yn00.tab [https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_1KFG_analyses_blob_master_Paralog_kaks_Aapi.yn00.tab&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=QQfC31p3Me-1RzS8aYNfIE0bYdnUkzAe0wipfYQBuFo&s=GrN7W6QsRnYM_SKDH7AyryL7klITTHHe9AP0mLqaiwM&e=]

scripts for the step are in here: https://github.com/1KFG/analyses/blob/master/Paralog/jobs [https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_1KFG_analyses_blob_master_Paralog_jobs&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=QQfC31p3Me-1RzS8aYNfIE0bYdnUkzAe0wipfYQBuFo&s=BU8D2euRkMvyb3-cRnEHpfwfgyb_BL0vgIuGq7YcNbw&e=]

On Wed, Jan 11, 2017 at 7:38 AM, Fields, Christopher J < cjfields at illinois.edu [cjfields at illinois.edu] > wrote:
On 1/11/17, 8:44 AM, "Bioperl-l on behalf of Carnë Draug" <bioperl-l-bounces+cjfields= illinois.edu at mailman.open-bio.org [illinois.edu at mailman.open-bio.org] on behalf of carandraug+dev at gmail.com [carandraug%2Bdev at gmail.com] > wrote:

>On 11 January 2017 at 04:45, Mark A. Jensen < maj at fortinbras.us [maj at fortinbras.us] > wrote:
>> And here it is -- still runs! No BioPerl required, as it turns out.
>>
>> https://github.com/majensen/dnds [https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_majensen_dnds&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=QQfC31p3Me-1RzS8aYNfIE0bYdnUkzAe0wipfYQBuFo&s=1_31hhX20PvtjmUa7apyJ-0mO8c1U9uCxSHWiRZrgEs&e=]
>>
>> MAJ
>
>This is great thank you. Since you are not packaging it, can I just
>copy it into my project? Or maybe adapt it to bioperl (any suggestion
>where it should go?) Also, can you please specify a license?
>
>Thank you
>Carnë

This might be something to ask Jason (cc’d). Jason, any ideas where dN/dS functionality might fit best in bioperl?

chris
>

--
Jason E Stajich, PhD
Associate Professor
University of California, Riverside
http://lab.stajich.org [https://urldefense.proofpoint.com/v2/url?u=http-3A__lab.stajich.org&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=QQfC31p3Me-1RzS8aYNfIE0bYdnUkzAe0wipfYQBuFo&s=j7Szq81HAht_yMoj3LXB0P0QbygXOroS76oaPXkfthI&e=] http://fungalgenomes.org [https://urldefense.proofpoint.com/v2/url?u=http-3A__fungalgenomes.org&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=QQfC31p3Me-1RzS8aYNfIE0bYdnUkzAe0wipfYQBuFo&s=8DU2Gq1QYWpqpTOqJnQt5ktJmz4fFM0O5BOKV3Fx5UQ&e=] http://fungidb.org [https://urldefense.proofpoint.com/v2/url?u=http-3A__fungidb.org&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=QQfC31p3Me-1RzS8aYNfIE0bYdnUkzAe0wipfYQBuFo&s=SubelrzDxlirP71goG-iuwgfik9ABj94k_jGKTj9ux8&e=] http://zygolife.org [https://urldefense.proofpoint.com/v2/url?u=http-3A__zygolife.org&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=QQfC31p3Me-1RzS8aYNfIE0bYdnUkzAe0wipfYQBuFo&s=j3RplXQeu4w-CfGHr12fD6nSX3jEtsXwNrQ0rXAoXo4&e=]
@stajichlab @hyphaltip @fungalgenomes @fungidb @zygolife
office: 951.827.2363
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/bioperl-l/attachments/20170111/a0dcab96/attachment.html>