Help with PROTML program in PHYLIP package?

Joe Felsenstein joe at
Mon Oct 24 19:23:13 EST 1994

In article <38grob$h6m at>,
Bernard Khoo <bcek1 at> wrote:
>I've recently been using the PHYLIP package (v 3.5) to construct trees
>based on protein sequence divergences, and the PROTML program seems to
>be the ticket.
>However, I've had problems getting it to run on my SGI (IRIX 5.0)
>Does anybody have any experience in getting this program to run under

It being in the Unsupported Division of PHYLIP I can't help you, except to
say that it is said to work a lot better if the REAL variables are
declared as DOUBLE instead.

But ... there is now a new version of PROTML from Adachi and Hasegawa.  It
is in C, and can be obtained by ftp in their package MOLPHY from their
site (  I would suggest you to try that

Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
 Internet:         joe at     (IP No.

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