Codon rate ML models

Joe Felsenstein joe at evolution.genetics.washington.edu
Fri Dec 11 15:09:27 EST 1998


[This is a repost as I have, once again, accidentally cancelled an
article by typing on the wrong key while using my news-reader]

In article <74ptu1$i57 at net.bio.net>,
John Huelsenbeck  <johnh at brahms.biology.rochester.edu> wrote:
[a most useful summary of the availability of models for Ml phylogenies
using codons, but I need to correct one detail:]

>I believe that DNAML has/had a feature allowing the user to assign
>sites to different categories, each with its own potential rate. Perhaps
>a citation of the PHYLIP manual may be appropriate.

DNAML in PHYLIP 3.5 does not do this.  DNAML in the previous version
did (v3.4) and in the next version it will be restored.  A beta release
should be out soon.  We eliminated it to make room for Hidden Markov
Model assignment of rates, but next we will add it back in while keeping
the HMMs too.

-- 
Joe Felsenstein         joe at genetics.washington.edu
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA




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