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Maximum Likelihood Analysis Question

Wnn System Account wnn at evolution.genetics.washington.edu
Mon Aug 19 14:34:07 EST 1996

In article <4va62e$1ija at uni.library.ucla.edu>,
Ron Kagan  <rkagan at ewald.mbi.ucla.edu> wrote:
>For those of you who have used maximum likelihood analysis (DNAML and
>DNAMLK of Felsenstein's Phylip package): What level of significance do
>you use for the likelihood ratio between the log likelihoods w and w/o
>the molecular clock, to reject the null hypothesis of the molecular
>clock?  Is p<0.05 still the standard, or should I use a stricter criteria

I don't think that a survey is quite the right thing to do here.  It is
a matter of how cautious you want to be.  If the statistical test is done
properly (which is an issue, of course), then P = 0.05 means that if there
is actually a molecular clock, you will falsely conclude that there isn't
5% of the time.  If you report your P value the reader can judge for
themselves, though given biologist's statistical backgrounds it might be wise
to mention that this is what the P value means.

So it is a bit a matter of taste.

Joe Felsenstein         joe at genetics.washington.edu     (IP No.
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

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