<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div>Hi Matthieu,</div><div><br></div><div>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.</div><div><br></div><div>Cheers,</div><div>álvaro</div><div><br></div>Message: 4<br>Date: Wed, 16 Apr 2014 14:30:07 +0100<br>From: Matthieu Muffato <<a href="mailto:muffato@ebi.ac.uk">muffato@ebi.ac.uk</a>><br>Subject: Re: [ensembl-dev] Nexus/Phylip file of sequenced species<br>To: Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>Message-ID: <<a href="mailto:534E85DF.9090006@ebi.ac.uk">534E85DF.9090006@ebi.ac.uk</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Hi ?lvaro,<br><br>Compara stores a few species tree in <br>ensembl-compara/scripts/pipeline/species_tree.*.nw in Newick format.<br><br>species_tree.eukaryotes.topology.nw is a binary tree with all the <br>species that we have in Ensembl, and without branch lengths.<br><br>The 3 species_tree.*.branch_len.nw files are also binary trees, but this <br>time with branch lengths computed from our multiple alignments. Again, <br>the species there are only the ones that we have in Ensembl<br><br>If you're interested in fish / sauropsids, we have an updated version on <br>the master branch, that fixes the position of the root node<br><br>Hope this helps,<br>Matthieu<br><br>On 15/04/14 09:14, Alvaro Martinez Barrio wrote:<br><blockquote type="cite">Hi,<br><br>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.<br><br>If you could please point me in the right direction I would be extremely thankful.<br><br>Best regards,<br>?lvaro</blockquote></body></html>