In article <email@example.com>,
Lee Weigt <weigt at FMPPR.FMNH.ORG> wrote:
>In article <4sgfu9$mcv at nntp3.u.washington.edu>,
>joe at evolution.genetics.washington.edu (Joe Felsenstein) writes:
>>> But however that is to be done in a likelihood framework, the RRT has
>> more problems as it cannot tell you how to combine all the
>> three-taxon tests.
>>In article <muse at kurtz.bio.psu.edu> writes
>>Agreed. BUT, that does not imply that doing many or all pairwise
>>comparisons is a useless thing to do. And, in fact, many of the tests
>>_are_ independent (this can be argued along the lines from Felsenstein's
>>1985 (?) article on independent contrasts).
>>Which tests are independent? When performing a multiple test correction,
>like the sequential Bonferroni, how do we decide what constitutes a family
>of tests that needs to be analyzed collectively? Should a family be
>defined as all those tests that have two similar taxa (outgroup and one
>ingroup)? Or should we combine all tests with a similar outgroup, which
>for 50 taxa and an alpha of .05 would make a "table-wide" alpha value of
Take one triple of taxa and draw the branches connecting them. Then do the
same for another triple of taxa. If there is any branch shared between them
(not just a point but a branch) then they are correlated. How much they
are correlated could be worked out with a statistical model.
But it is easier just to do the Likelihood Ratio Test rather than do that --
it takes all correlations into account properly, subject to the adequacy
of the its statistical model of sequence change.
Joe Felsenstein joe at genetics.washington.edu (IP No. 184.108.40.206)
Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA