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Dear Alison<br>
<br>
The branch lengths are based on a mixture of an estimation based on
4D sites and an estimation based on million years since the
divergence of two species (the data are taken from
<a class="moz-txt-link-abbreviated" href="http://www.timetree.org">www.timetree.org</a>).<br>
<br>
At UCSC and Ensembl, we have agreed to use the same species tree for
the alignments. However, we do not work exactly with the same set of
species. You can find more information here:
<span class="clickylink"><a target="new"
href="http://genomewiki.ucsc.edu/index.php/Human/hg19/GRCh37_46-way_multiple_alignment#4D_sites_branch_length_calculations">http://genomewiki.ucsc.edu/index.php/Human/hg19/GRCh37_46-way_multiple_alignment#4D_sites_branch_length_calculations</a></span><br>
<br>
Additional species are included in the middle of an existing branch.
An initial estimation of the branch lengths is based on the million
years since the divergence of two species, the data being taken from
<a class="moz-txt-link-abbreviated" href="http://www.timetree.org">www.timetree.org</a>.
<br>
<br>
I hope this helps<br>
<br>
Javier<br>
<br>
On 24/04/12 17:23, Alison Wright wrote:
<blockquote
cite="mid:230613BF49EDA647A5BB3A4DB65CABDE02E702@MBX06.ad.oak.ox.ac.uk"
type="cite">
<pre wrap="">Hi,
I have accessed the Ensembl Species Tree generated for use in Phylowidget by the Compara team (which includes all the current species for the main Ensembl website, plus a few additional mammalian species of interest).
However, I cant find out what the branch lengths represent (number of substitutions per site? PAM units?) and how they were calculated?
Thanks very much for any help.
Alison Wright
</pre>
<br>
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<br>
<pre wrap="">_______________________________________________
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK</pre>
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