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Relative rate test

Lee Weigt weigt at FMPPR.FMNH.ORG
Thu Jul 18 12:29:09 EST 1996

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

Michael Nedbal
Geology Department
Field Museum of Natural History
Roosevelt Road at Lake Shore Drive
Chicago, IL 60605-2496
nedbal at fmppr.fmnh.org
312-922-9410 Ext 545

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