[ensembl-dev] Conservation_scores ?

[Sébastien Moretti]

> No, the conservation scores are calculated from the genomic alignments.
>
> For closely related subtrees in the MCoffee genetree alignments, there
> are SiteWise_dNdS values available calculated using SLR (Massingham et
> al.).
>
> There is also a table of "alignment scores" in
> protein_tree_member_score, but those are alignment quality/uncertainty
> measures, not conservation measures.

I didn't want to talk about conservation measures but alignment quality, 
sorry.

In protein_tree_member_score table, do you mean MCoffee scores per 
residue (score_ASCII output) ?

> Cheers,
>
> Albert Vilella.
>
> On Wed, 2010-09-29 at 14:53 +0200, Sébastien Moretti wrote:
>> Hi
>>
>> does ensembl_compara_59.conservation_scores table contain scores related
>> to MCoffee family alignments ?
>>
>> Regards

-- 
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/