[ensembl-dev] Ictidomys tridecemlineatus species name
Matthieu Muffato
muffato at ebi.ac.uk
Thu Jul 25 09:46:10 BST 2013
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.
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
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