Max Like for Amino Acid seqs

Joe Felsenstein joe at evolution.genetics.washington.edu
Thu Sep 19 11:13:02 EST 1996

In answer to the original question I had declared that:
>> Two programs exist to do it.  Ziheng Yang's PAML and Adachi and Hasegawa's
>> MOLPHY package.

In article <Pine.A32.3.91.960919094515.27528A-100000 at gsaix2.cc.GaSoU.EDU>,
Q. Quentin Fang <qfang at GSAIX2.CC.GASOU.EDU> wrote:
>How about Puzzle 2.5, a maximum likelihood program for both nucleotides and 
>a.a.?  Has anyboy tried the program?

PUZZLE is clearly a third alternative.  It looks first at four-species trees
but then does do an overall tree on a likelihood basis, so I certainly should
have included it in the list.

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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