[ensembl-dev] phyloFit model files

Christian Groß - EWI C.Gross at tudelft.nl
Mon Nov 20 11:41:29 GMT 2017

Dear Matthieu,

Thank you very much, I think that I know how I have to proceed further. The .mod file is the output of phyloFit consisting of the computed tree with branch lengths, substitution matrix and nucleotide equilibrium frequencies. 

 Best regards,


-----Original Message-----
From: Matthieu Muffato [mailto:muffato at ebi.ac.uk] 
Sent: maandag 20 november 2017 10:09
To: Ensembl developers list; Christian Groß - EWI
Subject: Re: [ensembl-dev] phyloFit model files

Hi Christian

Sorry but the information is slightly out-of-date. We are not using phyloFit any more. Branch lengths now come either Mash or RAxML.

I've had a look at the command-line we used to run phyloFit, but I'm not sure what the .mod file is. We were doing: "$phylofit_exe --tree $species_tree_file --subst-mod HKY85 --out-root $phylo_out_file $msa_fasta_file"


On 20/11/17 02:59, Christian Groß - EWI wrote:
> 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,
> Christian
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Matthieu Muffato, Ph.D.
Ensembl Compara and TreeFam Project Leader European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus, Hinxton Cambridge, CB10 1SD, United Kingdom Room  A3-145 Phone + 44 (0) 1223 49 4631
Fax   + 44 (0) 1223 49 4468

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