[ensembl-dev] Gerp conservatioon scores & gerp neutral evolution scores

[Matthieu Muffato]

Hi Christian

First, note that we are using Gerp 2.1, not gerp++

The score shown in the alignment file is the difference between the 
observed conversation score and the expected one. The two values 
original values are only available using the API

 From the per-column conservation scores, gerp also defines constrained 
elements. They are available as BED files 
ftp://ftp.ensembl.org/pub/release-91/bed/ensembl-compara/11_teleost_fish.gerp_constrained_elements/ 
and with the Perl API, but only the latter enables access to the p-value

Matthieu

On 22/02/18 14:47, Christian Groß - EWI wrote:
> Dear Dev Team,
> 
> I have a question regarding the Gerp conservation scores which you 
> report in your multiple alignment .emf files.
> 
> ftp://ftp.ensembl.org/pub/current_emf/ensembl-compara/multiple_alignments/
> 
> The reported score is the Gerp conservation score, I assume the rejected 
> substitution score, how it is called in the Gerp++ publication 
> (http://mendel.stanford.edu/SidowLab/pdfs/2010DavydovEtAl.pdf). Do you 
> also have the Gerp Neutral Evolution scores for download or the p-Values 
> for constrained elements? If possible I would be pretty interested in 
> those too.
> 
> Thank you very much for the service you provide.
> 
> Best regards,
> 
> Christian Gross
> 
>