Steve Hardies wrote (as part of a longer post):
> Now my question is, what happens if you merge divergent sequences
> with saturated transitions into data with more closely related sequences?
> Will the liklihood curve for Ts/Tv broaden over what it would have been
> with the closely related sequences alone? That is, will you convert
> uncertainty about the divergent branch lengths into uncertainty about
> the global Ts/Tv?
I would think that it will not broaden. If you add to data that implies a
given amount of uncertainty about Ts/Tv ratio some more distant sequences that
would be compatible with any Ts/Tv ratio, surely the uncertainty gets no worse,
as in effect one is adding irrelevant data, and the likelihood method
Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
Internet: joe at genetics.washington.edu (IP No. 184.108.40.206)