tag:treefam.tenderapp.com,2013-02-16:/discussions/problems/59-amphimedon-accessionsTreeFam: Discussion 2018-01-31T18:37:17Ztag:treefam.tenderapp.com,2013-02-16:Comment/446273142018-01-30T16:46:22Z2018-01-30T16:46:22ZAmphimedon accessions<div><p>Dear Emily</p>
<p>TreeFam 9 included the JGI geneset from October 2010, as found in Ensembl Metazoa version 16. It uses Aqu1.* identifiers for genes and PAC_* identifiers for proteins.<br>
In 2015, a new version of the annotation was released (<a href="http://europepmc.org/abstract/MED/25975661">http://europepmc.org/abstract/MED/25975661</a> ) with Aqu2.* identifiers for both genes and proteins. This is the version now used in Ensembl Metazoa (although the old version is still available as an optional track). I couldn't see any mapping between the old geneset and the new one on Degnan lab's download page: <a href="http://amphimedon.qcloud.qcif.edu.au/downloads.html">http://amphimedon.qcloud.qcif.edu.au/downloads.html</a><br>
You may want to directly contact the authors of the paper.</p>
<p>Regards,<br>
Matthieu Muffato</p></div>Matthieu Muffatotag:treefam.tenderapp.com,2013-02-16:Comment/446273142018-01-30T21:44:49Z2018-01-30T21:44:49ZAmphimedon accessions<div><p>On 31 Jan 2018, at 02:46, Matthieu Muffato > wrote:</p>
<p>Hi Mathieu</p>
<p>Do you know when a new version of term will be run?</p>
<p>Thanks</p>
<p>Emily</p></div>Emily Wongtag:treefam.tenderapp.com,2013-02-16:Comment/446273142018-01-31T18:37:16Z2018-01-31T18:37:16ZAmphimedon accessions<div><p>Hi Emily</p>
<p>Treefam is in the middle of a reorganization of the phylogenetic analyses of Ensembl and Ensembl Genomes. We have generated a new library of HMMs that are going to be used across all Ensembl sites later this year (see <a href="http://www.ensembl.org/info/genome/compara/hmm_lib.html">http://www.ensembl.org/info/genome/compara/hmm_lib.html</a> and <a href="ftp://ftp.ensembl.org/pub/current_compara/">ftp://ftp.ensembl.org/pub/current_compara/</a> )<br>
At the moment we don't know how the treefam.org website is going to change.</p>
<p>Kind regards,<br>
Matthieu</p></div>Matthieu Muffato