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Making alignments

Joe Staton jstaton at oeb.harvard.edu
Wed Jan 21 11:18:56 EST 1998

>In article <6a30e6$ro7 at net.bio.net> "Guy A. Hoelzer" <hoelzer at med.unr.edu>
>  >This seems to me to be an overly optimistic view of the value of maximum
>  >likelihood approaches.  In general, maximum likelihood is vulnerable to
>  >errors in the chosen model of evolution and in the parameter estimates
>  >that are used.
>Agreed. But on the other hand: a phylogenetic inference method that is
>/not/ sensitive to the chosen model of evolution would be...?
>- Sean Eddy, Ph.D.
>- Dept. of Genetics, Washington University School of Medicine
>- 660 S. Euclid Box 8232, St. Louis MO 63110, USA
>- mailto://eddy@genetics.wustl.edu http://genome.wustl.edu/eddy

Hoelzer's point was not the sensitivity of the evolutionary model in
general, but the specific model that a maximum likelihood method uses to
calculate the tree to begin with.  If the model of molecular evolution is
wrong or the parameters needed for the model are poorly estimated, it's a
case of garbage in yields garbage out (albeit powerfully calculated

The model of evolution is another consideration, altogether (i.e.,
parsimony) which MAY be more robust to giving information about
evolutionary patterns even if not completely correct. (no flames please)

Joseph L. Staton, Ph. D.
Department of Invertebrate Zoology
Museum of Comparative Zoology
Harvard University
26 Oxford Street
Cambridge, MA 02138

Phone: 617-495-2447
Fax: 617-495-5667

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