In article <v01530501aefc07190637@[128.227.25.52]>,
Sam <abass at ICBR.IFAS.UFL.EDU> wrote:
>... Is there a standard
>method for calculating transition transversion ratios? For example if you
>do not want to assume the state of a hypothetical ancestor, then does one
>choose the most parsimonious solution for a given position or all
>possibilities?
The best way is to fit the tree using maximum likelihood, at a given
transition/transversion ratio (which you feed in as a parameter of the method).
Then record the likelihood. Do it at other Ts/Tv ratios, and record.
The maximum likelihood estimate of the Ts/Tv ratiion is the one that
achieves the highest likelihood.
This can be done by a number of runs of my program DNAML or by a single
run of David Swofford's forthcoming PAUP*.
This approach solves the problems of deciding among alternative
numbers of transitions and transversions that would be needed to
explain a given set of nucleotides at one site, without any arbitrary
decisions.
--
Joe Felsenstein joe at genetics.washington.edu (IP No. 128.95.12.41)
Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA
