<p dir="ltr" style="margin-top:0; margin-bottom:0;">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.<br>
Mark<br><br></p>
<div class="cm_quote" style=" color: #787878">On Wed, Jan 11, 2017 at 1:25pm, Fields, Christopher J <<a href="mailto:cjfields@illinois.edu">cjfields@illinois.edu</a>> wrote:</div><br><div id="oldcontent" style="background: rgb(255, 255, 255);"><blockquote style="">
<div>Thanks Jason!</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>chris</div>
<div><br>
</div>
<span id="OLK_SRC_BODY_SECTION">
<div style="font-family:Calibri; font-size:12pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt">
<span style="font-weight:bold">From: </span>Jason Stajich <<a href="mailto:jason.stajich@ucr.edu">jason.stajich@ucr.edu</a>><br>
<span style="font-weight:bold">Date: </span>Wednesday, January 11, 2017 at 9:52 AM<br>
<span style="font-weight:bold">To: </span>Chris Fields <<a href="mailto:cjfields@illinois.edu">cjfields@illinois.edu</a>><br>
<span style="font-weight:bold">Cc: </span>Carnë Draug <<a href="mailto:carandraug+dev@gmail.com">carandraug+dev@gmail.com</a>>, Mark Jensen <<a href="mailto:maj@fortinbras.us">maj@fortinbras.us</a>>, bioperl mailing list <<a href="mailto:bioperl-l@mailman.open-bio.org">bioperl-l@mailman.open-bio.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [Bioperl-l] free software to estimate dS and dN in pairwise comparisons<br>
</div>
<div><br>
</div>
<blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;">
<div>
<div>
<div dir="ltr">
<div>Hi - As standalone non-bioperl dependent it seems like it needs it own repo?</div>
<div><br>
</div>
<div>Currently we have Ka/Ks calculation in Bio::Align::DNAStatistics - not sure if this implementation is faster? <br>
</div>
<div><br>
</div>
FYI Carnë - you might also see my fast C implementation pairwise dnds as well that is a hybrid of the yn00 code.
<div><a href="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=">https://github.com/hyphaltip/subopt-kaks</a><br>
</div>
<div>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.</div>
<div><a href="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=">https://github.com/1KFG/analyses/blob/master/Paralog/kaks/Aapi.yn00.tab</a><br>
</div>
<div><br>
</div>
<div>scripts for the step are in here:</div>
<div><a href="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=">https://github.com/1KFG/analyses/blob/master/Paralog/jobs</a><br>
</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Jan 11, 2017 at 7:38 AM, Fields, Christopher J <span dir="ltr">
<<a href="mailto:cjfields@illinois.edu">cjfields@illinois.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
On 1/11/17, 8:44 AM, "Bioperl-l on behalf of Carnë Draug" <bioperl-l-bounces+cjfields=<a href="mailto:illinois.edu@mailman.open-bio.org">illinois.edu@mailman.open-bio.org</a> on behalf of
<a href="mailto:carandraug%2Bdev@gmail.com">carandraug+dev@gmail.com</a>> wrote:<br>
<br>
<br>
<br>
>On 11 January 2017 at 04:45, Mark A. Jensen <<a href="mailto:maj@fortinbras.us">maj@fortinbras.us</a>> wrote:<br>
>> And here it is -- still runs! No BioPerl required, as it turns out.<br>
>><br>
>> <a href="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=" rel="noreferrer">
https://github.com/majensen/dnds</a><br>
>><br>
>> MAJ<br>
><br>
>This is great thank you. Since you are not packaging it, can I just<br>
>copy it into my project? Or maybe adapt it to bioperl (any suggestion<br>
>where it should go?) Also, can you please specify a license?<br>
><br>
>Thank you<br>
>Carnë<br>
<br>
This might be something to ask Jason (cc’d). Jason, any ideas where dN/dS functionality might fit best in bioperl?<br>
<br>
chris<br>
><br>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr"><span style="font-size:x-small">Jason E Stajich, PhD </span><br style="font-size:x-small">
<span style="font-size:x-small">Associate Professor</span><br style="font-size:x-small">
<span style="font-size:x-small">University of California, Riverside</span><br style="font-size:x-small">
<span style="font-size:x-small"><a href="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://lab.stajich.org</a><a href="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://fungalgenomes.org</a> <a href="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://fungidb.org</a> <a href="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=">
http://zygolife.org</a></span><br style="font-size:x-small">
<span style="font-size:x-small">@stajichlab @hyphaltip @fungalgenomes @fungidb @zygolife</span><br style="font-size:x-small">
<span style="font-size:x-small">office: 951.827.2363</span><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</span>
<div><br>
</div>
<div>
<div>
<div><br>
</div>
<div>
<div id="MAC_OUTLOOK_SIGNATURE"></div>
</div>
</div>
</div>
</blockquote></div>