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transition/transversion calc?

Joe Felsenstein joe at GENETICS.WASHINGTON.EDU
Sun Aug 14 19:00:18 EST 1994

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.

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