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Joe Felsenstein joe at evolution.genetics.washington.edu
Mon Jun 14 12:44:17 EST 1999

In article <7k35gt$4kg at net.bio.net>, Luis  <luismms at mail.telepac.pt> wrote:
>While checking the .doc files from the PHYLIP package I came across with
>the documentation file of a pascal program called PROTML (Maximum
>Likelihood Inference of Protein Phylogeny) by Jun Adachi and  Masami
>Hasegawa which is not included in the package, can ayone tell me how to
>get this program?

Although an old Pascal version is distributed in source code as part of the
PHYLIP package, I would recommend you get it from the original authors in
its updated form (in C rather than Pascal, and also available as some kinds of
executables).  You can get it by ftp from    sunmh.ism.ac.jp.  You can also
find Windows95 executables at


>By the way, another question, does anyone know how to get branch lenght
>estimates using the parsimony or maximum likelihood methods in th PHYLIP

Yes.  The maximum likelihood estimates of branch length are printed out in
the maximum likelihood programs of PHYLIP.  It is impossible not to see
them when you run the program.

The parsimony programs fore the present do not produce branch length estimates.
Some of them will in the next release.  In the meantime, the best you can do
(aside from using someone else's programs) is to take the tree that they
produce, use the PHYLIP program Retree to make it unrooted, then use it as
a User Tree in program Fitch, with a distance matrix derived from the same
characters.  That will give approximate branch lengths.

I note that the answers to both of these questions are at the PHYLIP web
site, one in the Frequently Asked Questions page, and the other in the
Phylogeny Programs pages.

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

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