[ensembl-dev] Can't find primate multispecies alignment on ftp

[Matthieu Muffato]

Dear Jack,

The latest primate alignment (8 genomes) is only available in MAF 
format: 
ftp://ftp.ensembl.org/pub/release-90/maf/ensembl-compara/multiple_alignments/epo_8_primate/
The ancestral alleles we've derived from it are available at 
ftp://ftp.ensembl.org/pub/release-90/fasta/ancestral_alleles/

FYI, since Ensembl 76 we've added the Vervet Monkey/African Green Monkey

Regards,
Matthieu


On 14/10/17 11:07, Jack Kamm wrote:
> Dear all,
> 
> I can't find the 8-primate multispecies alignment on 
> ftp://ftp.ensembl.org/pub/release-90/emf/ensembl-compara/multiple_alignments/. 
> 
> 
> There is a 7-primate multispecies alignment in release 76, 
> (ftp://ftp.ensembl.org/pub/release-76/emf/ensembl-compara/epo_7_primate/), 
> but subsequent releases seem to be missing this directory. The release 
> 76 version suffices for my purposes, but I would prefer to use the most 
> recent version if possible.
> 
> I'm using the multispecies alignment to get human ancestral alleles 
> aligned to grch38. If there is an ancestral alleles FASTA somewhere that 
> would also be quite useful. But, I'd still like the multispecies EMF 
> files so I can compare different ways of calling the ancestral allele.
> 
> Thanks,
> Jack Kamm
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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