[ensembl-dev] Nexus/Phylip file of sequenced species

[Alvaro Martinez Barrio]

Hi Matthieu,

It helped! This is the information about the files I was looking for. Thanks! I will have a look at those tree files in newick format.

Cheers,
álvaro

Message: 4
Date: Wed, 16 Apr 2014 14:30:07 +0100
From: Matthieu Muffato <muffato at ebi.ac.uk>
Subject: Re: [ensembl-dev] Nexus/Phylip file of sequenced species
To: Ensembl developers list <dev at ensembl.org>
Message-ID: <534E85DF.9090006 at ebi.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi ?lvaro,

Compara stores a few species tree in 
ensembl-compara/scripts/pipeline/species_tree.*.nw in Newick format.

species_tree.eukaryotes.topology.nw is a binary tree with all the 
species that we have in Ensembl, and without branch lengths.

The 3 species_tree.*.branch_len.nw files are also binary trees, but this 
time with branch lengths computed from our multiple alignments. Again, 
the species there are only the ones that we have in Ensembl

If you're interested in fish / sauropsids, we have an updated version on 
the master branch, that fixes the position of the root node

Hope this helps,
Matthieu

On 15/04/14 09:14, Alvaro Martinez Barrio wrote:
> Hi,
> 
> Is there anywhere that I could find a nexus/phylip file for the phylogeny of the species (specifically metazoan) from the full genome comparisons? I think this should be done somewhere as in one page you have an unrooted tree produced with Dendroscope.
> 
> If you could please point me in the right direction I would be extremely thankful.
> 
> Best regards,
> ?lvaro
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