[Bioperl-l] PAML::Codeml outputs unstable value, why?

[Roy Chaudhuri]

Hi Xianjun,

I'm not sure if it is the cause of your problem, but your sequences seem
to be quite short. This paper:
http://mbe.oxfordjournals.org/cgi/content/full/21/12/2290

suggests that the codeml method of calculating Ka and Ks may be
unreliable for sequences shorter than 300 codons.

Roy.
--
Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.