[ensembl-dev] gerp conservation scores

[Javier Herrero]

Hi Alison

It uses one single tree for regions where no segmental duplications have been 
detected by the pipeline. In every region where the EPO pipeline detects 
segmental duplications, we need a specific tree for that locus. We use semphy 
to estimate a tree from the alignment and uses this as an input to GERP.

I hope this helps

Javier

On Friday 11 Mar 2011 10:36:49 Alison Meynert wrote:
> When calculating Gerp conservation scores, does the Compara pipeline use
> a single tree to describe the neutral rate, or does it vary the tree
> according to the locus?
> 
> Cheers,
> Alison

-- 
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK