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.A220.127.116.110919094515.27528A-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. 18.104.22.168)
Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA