[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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