[ensembl-dev] COMPARA for (local) orthology detection

Celine Scornavacca celine.scornavacca at umontpellier.fr
Tue Mar 22 10:10:44 GMT 2016

Hi all,

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.

The part of the protocol that interests me should be this one:

/*Protein trees*//are constructed using a representative protein for
every gene in Ensembl: proteins are clustered using //hcluster_sg
and each cluster of proteins is aligned using //M-Coffee
//Mafft <http://mafft.cbrc.jp/alignment/software/>//. Finally,
//TreeBeST <https://github.com/Ensembl/treebest>//is used to produce a
gene tree from each multiple alignment, reconciling it with the species
tree to call duplication events//
/[from http://www.ensembl.org/info/genome/compara/index.html]

Is it possible to find somewhere the tools/scripts with the correct
parameters to do the same thing but locally and on our data?

Best regards,

New Email Address: celine.scornavacca at umontpellier.fr

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

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