Joe Felsenstein writes (in response to a question by Tom Doak):
>By doing multiple runs with DNAML from PHYLIP, at each at a different value
>of the transition/transversion ratio, and picking the result that achieves the
>highest likelihood, and also saving that tree, one will get a joint ML
>estimate of the ratio and the tree. I think that is what you want.
Do you think it would be useful (when using the above method) to obtain
the transition/transversion ratio from a subset of the most closely
related sequences to suppress noise caused by saturation of
transitions at greater divergence?
Steve Hardies, Dept. of Biochem. Univ. of Texas HSC at San Antonio
Hardies at thorin.uthscsa.edu