[ensembl-dev] phyloFit model files

Christian Groß - EWI C.Gross at tudelft.nl
Mon Nov 20 02:59:05 GMT 2017

Dear Ensembl Developer Team,

My name is Christian Groß and I am a researcher at TU Delft, the Netherlands.

I am currently trying to compute PhyloP & PhastCon scores (from the PHAST Package) for some of your alignments (21 eutherian mammals EPO, 53 eutherian mammals EPO_LOW_COVERAGE, 4 sauropsids EPO,  7 sauropsids EPO_LOW_COVERAGE). To utilize PhyloP and PhastCon I need model files created by phyloFit (another program from the PHAST Package). These model files contain a substitution rate matrix, a tree with branch lengths and estimates of nucleotide equilibrium frequencies.
On your website (https://www.ensembl.org/info/genome/compara/index.html#species_tree) below “Species tree” it is mentioned that you ran phyloFit to compute branch lengths to be able to compute constrained regions via Gerp. Besides of the species trees with branch lengths, I have not been successful in finding any other data generated by phyloFit via ftp or API. Is it possible to provide the .mod files generated by phyloFit or any log file which gives information about the set parameters?

If you could help me in this matter you would help me a great deal.

Best regards,


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20171120/a6b87431/attachment.html>

More information about the Dev mailing list