In article <32ocpm$3ko at u.cc.utah.edu> Tom Doak <tom_doak at hlthsci.med.utah.edu> writes:
>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
>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.
Hmmm.... I think I see your train of thought. Even the original post
suggests this as well. You must understand that the notion of transitions
and transversions MUST stand in relation to some tree. After all the
site has to change from something to something, thus one needs to
ask at the very least "from what?" This requires a phylogenetic
hypothesis of some sort - ergo a tree.
Mark E. Siddall "I don't mind a parasite...
mes at vims.edu I object to a cut-rate one"
Virginia Inst. Marine Sci. - Rick
Gloucester Point, VA, 23062