[Bioperl-l] Re: Comparative genomics - regions of synteny and whole genome duplication

[Ian Holmes]

Elia Stupka wrote:

> This is the strategy that I had outlined, which leaves us with the major
> question of assigning orthologues.

There is an algorithm from the Eddy group to classify genes into
orthologues/paralogues (i.e. locate duplication events) given two trees:
the species tree and the gene sequence similarity tree. The definition of
orthology allows for completely automated classification.

There is an implementation at

http://www.genetics.wustl.edu/eddy/forester/

Ian