Tom Doak writes:
> While there are various programs that will use values for transitions vs
> transversions, we haven't been able to find a program that produces these
> values. MacClade does something of the sort, but the values are based on
> a tree, and we would like to use them to create the tree. Programs in
> Phylip also allow one to set these values, but again it's not clear that
> there is anything in the package that calculates the values.
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.
Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
Internet: joe at genetics.washington.edu (IP No. 18.104.22.168)