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

[James Allen]

Hello Álvaro,
From a metazoan perspective, the only species tree we have is a pruned version of the NCBI taxonomy (there are no multiple genome alignments with which to define any other species tree, or any branch lengths on the NCBI tree). The pruned NCBI tree isn't currently available for download from the Ensembl Metazoa site; I've attached a copy in Newick format.

Cheers,
James


On Wed, 16 Apr 2014 14:30:07 +0100
Matthieu Muffato <muffato at ebi.ac.uk> wrote:

> Hi Álvaro,
> 
> 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,
> > álvaro
> 
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