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transition/transversion calc?

Joe Felsenstein joe at GENETICS.WASHINGTON.EDU
Mon Aug 15 17:32:11 EST 1994

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
knows that.

Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
 Internet:         joe at genetics.washington.edu     (IP No.

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