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<div class="moz-text-html" lang="x-unicode"> Hi all,<br>
<br>
I am interested to install COMPARA locally to obtain, starting
with a batch of files - each one containing a set of sequences for
a same species, a list of orthologs pairs.<br>
<br>
The part of the protocol that interests me should be this one:<br>
<br>
<i><strong>Protein trees</strong></i><i> are constructed using a
representative protein for every gene in Ensembl: proteins are
clustered using </i><i><a rel="external"
href="http://treesoft.svn.sourceforge.net/viewvc/treesoft/branches/lh3/hcluster/">hcluster_sg</a></i><i>
based on </i><i><a rel="external"
href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download">NCBI
BLAST+</a></i><i> e-values, and each cluster of proteins is
aligned using </i><i><a rel="external"
href="http://www.tcoffee.org/Projects_home_page/m_coffee_home_page.html">M-Coffee</a></i><i>
or </i><i><a rel="external"
href="http://mafft.cbrc.jp/alignment/software/">Mafft</a></i><i>.
Finally, </i><i><a rel="external"
href="https://github.com/Ensembl/treebest">TreeBeST</a></i><i>
is used to produce a gene tree from each multiple alignment,
reconciling it with the species tree to call duplication events</i><i><br>
</i>[from <a class="moz-txt-link-freetext"
href="http://www.ensembl.org/info/genome/compara/index.html">http://www.ensembl.org/info/genome/compara/index.html</a>]<br>
<br>
Is it possible to find somewhere the tools/scripts with the
correct parameters to do the same thing but locally and on our
data?<br>
<br>
Best regards,<br>
<br>
<br>
<br>
</div>
<pre class="moz-signature" cols="72">--
New Email Address: <a class="moz-txt-link-abbreviated" href="mailto:celine.scornavacca@umontpellier.fr">celine.scornavacca@umontpellier.fr</a>
Celine Scornavacca
Chargé de Recherche - CNRS
Institut des Sciences de l'Evolution - CC64
Université Montpellier
Place Eugène Bataillon
34095 Montpellier, France
Tel : +33 (0)4 67 14 36 97
</pre>
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