Making alignments

Guy A. Hoelzer hoelzer at med.unr.edu
Wed Jan 21 12:43:06 EST 1998


In article <6a33ft$54t at net.bio.net>, Sean Eddy <eddy at wol.wustl.edu> wrote:

> In article <6a30e6$ro7 at net.bio.net> "Guy A. Hoelzer"
<hoelzer at med.unr.edu> writes:
>   >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...? 

That is my point exactly.  I have been increasingly concerned that ML has
been portrayed as somehow immune to some the the "universal" problems in
phylogeny estimation.  Given its mathematical complexity, I believe that
many practitioners of phylogenetics are judging ML based on the summary
statements of the experts, so a more balanced portrayal is essential.

-- 
Guy Hoelzer                              e-mail:  hoelzer at med.unr.edu
Department of Biology                    phone:   702-784-4860
University of Nevada Reno                fax:     702-784-1302
Reno, NV  89557




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