testing if seqs. are in same phylo. tree?

Nick Goldman N.Goldman at gen.cam.ac.uk
Mon Nov 13 04:50:57 EST 1995

In article <480q62$1auj at hearst.cac.psu.edu>, Spencer Muse
<muse at kurtz.bio.psu.edu> wrote:

>  Having said that, it is, of course, of no concern since we must use
>  a Monte Carlo approach to evaluate the p-values anyway. And as 
>  another somewhat irrelevant aside, it seems that Goldman's claim
>  about the unsuitability of the chi-squaare approximation was a bit
>  too strong. A number of us have found this approximation to be quite 
>  good when yop have fully-specified null and alternative models. I
>  think that slight correction might have even popped up in a Goldman
>  and Yang paper somewhere along the way.

Yes, it has.  Thanks for the excuse to do some publicity, Spencer:

Yang, Z., Goldman, N., & Friday, A.  1995.  Maximum likelihood trees from
     DNA sequences:  a peculiar statistical estimation problem.
     Systematic Biology 44(3):384-399.

See in particular pp.393-394 (& cf. pp.390-393).

Nick Goldman
Dept of Genetics
Univ of Cambridge

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