[Bioperl-l] ortholog identification for many species

[Martin Lercher]

Hi,

I have to identify a large number of orthologs for a dozen or so species.
There was a discussion on the identification of orthologs here some months
ago (and  I got some information from Elia on the approach they took for the
Fugu project); however, my impression is that the methods discussed there
were more useful for a 2-species problem.

My feeling is that to identify orthologs in many species, one has to draw a
phylogenetic tree for all homologous sequences, and look for clusters of
genes that contain exactly one gene for each species (or, if more than one
gene for one species, these should be clustered together). Has anything
similar to this approach been implemented in Bioperl (or at all)? Or would
you suggest a different approach?

Cheers,
Martin
________________________

Martin Lercher, Ph.D.
Department of Biology and Biochemistry
University of Bath
Claverton Down
Bath,  Somerset
BA2 7AY, UK
Tel. +49-178-2573652
Fax +44-1225-386779
email: m.j.lercher@bath.ac.uk