Help with PROTML program in PHYLIP package?

Tim Littlejohn tim at megasun.BCH.UMontreal.CA
Mon Oct 24 22:17:28 EST 1994

In article <38grob$h6m at lyra.csx.cam.ac.uk> bcek1 at mole.bio.cam.ac.uk (Bernard Khoo) writes:
>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)
>system. From what I can make out of the source code (I taught myself
>small amounts of PASCAL a long, long time ago) it seems to require an
>input file called 'seqdata'; however, when I run the program it doesn't
>seem to be able to read in this file.

This is the case only for the older pascal version.

>Does anybody have any experience in getting this program to run under

Yes, with SunOS- the program has been completely rewritten in C, and
the new version of the package (called molphy) can be obtained by gopher.
Connect to:

    URL: gopher://megasun.bch.umontreal.ca:70/11/CMB/Phylogeny/Protml

or by anonymous ftp to sunmh.ism.ac.jp (
and look in /pub  for the molphy files.

I also have a SunOS executable at the gopher site listed above.

I hope this helps,

Tim Littlejohn

E-mail:     tim at bch.umontreal.ca  

Snail Mail: Departement de biochimie        Phone: (514) 343-6111, x5149
            Universite de Montreal          Fax:   (514) 343-2210 
            C.P. 6128, Centre-ville
            Montreal (Quebec), H3C 3J7

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