[ensembl-dev] Ictidomys tridecemlineatus species name

[Sébastien MORETTI]

Le 25.07.13 10:46, Matthieu Muffato a écrit :
> On 24/07/13 13:02, Sébastien Moretti wrote:
>> Hi
>>
>> It looks you use Ictidomys tridecemlineatus as species name in your
>> species tree http://www.ensembl.org/info/about/species.html but for the
>> same taxid the ensembl API returns one of its alias as scientific_name
>> (i.e. Spermophilus tridecemlineatus)
>>
>> Also, according to NCBI taxonomy, this species is a Sciurognathi and
>> should be grouped with mouse, rat and Dipodomys ordii in your species
>> tree. Currently it is out of this group, with other Rodentia.
>>
>> Regards
>>
>
> Hi Sébastien
>
> The current scientific name of our squirrel genome is now Ictidomys
> tridecemlineatus, but it was Spermophilus tridecemlineatus several
> releases ago.
> The species tree image has not been updated accordingly, regarding both
> the name and the phylogenetic position. We'll fix that for the next
> release.

Good

> For the gene trees, the species tree is always freshly built from the
> NCBI database, and the squirrel is indeed considered as a Sciurognathi.
> For the EPO alignments, we are using the wrong (old) topology, but it
> only affects the GERP results, not the alignments.
>
> Hope this helps,
> Matthieu

It helps a lot.
Thanks for your efforts

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://bioinfo.unil.ch/