[Bioperl-l] calculating the Ka/Ks ratio

[Darren Obbard]

Hi all,

Is there a module that will take a pair of aligned (coding) sequences, and 
report the Ka/Ks ratio? (non-synonymous mutations per non-synonymous site / 
synonymous mutations per synonymous site).

I appreciate that PAML will give me an ML estimate of Ka/Ks, but I'm aiming 
to do a sliding-window analysis and don't wish to send each window to PAML 
individually, - I  wondered whether there may be a quicker alternative.

Thanks,

Darren
--
Darren Obbard
Institute of Evolutionary Biology
University of Edinburgh, UK
darren.obbard at ed.ac.uk