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TR/TV ratio

Joe Felsenstein joe at evolution.genetics.washington.edu
Sun Jan 12 03:27:10 EST 1997


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



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