Subject: Re: transition/transversion calc?
From: Joe Felsenstein, joe at GENETICS.WASHINGTON.EDU
A number of good answers, but I'm realizing that I may have asked the
wrong question. And the right question may not have an answer. We are
working in a ciliated protozoa that is quit GC poor, and so we expect
there to be a bias in the freq of different mutations, which lead me to
ask about transition/transversions, but of course that's not how one gets
to be GC poor, or rather, just a two parameter model isn't enough, as I
understand it. So is the answer that we just not worry about it?
By the way, what we are currently doing is not so much tree building, but
calculations of divergence and synonymous vs nonsynonymous to try to show
conservation of a coding region.
Thanks so much,
tom_doak at hlthsci.med.utah.edu