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Molphy problem

Kerstin Hoef-Emden kerstin.hoef-emden at uni-koeln.de
Wed Sep 18 04:10:06 EST 2002


Gustavo Parisi <gustavo at unq.edu.ar> wrote:

> We have some problem to run molphy (v. 2.3b3) under linux. We tried to
> run the following commands

> protml -I -jf -R -n 1000  seqfile topolgyfile
> using different numbers of sequences the program generates a
> segmentation fault after a few topology evaluations. We have the same

I encountered similar problems with Molphy. Distance analyses worked out,
but ML crashed always. What hardware platform do you use? Mine is an Alpha
workstation running under Linux, thus I thought the source may not be 64-bi=
clean. Since I am no informatics person, my work around was to switch to
PAML. In contrast to Molphy (1996?) it is constantly updated (last update
was Version 3.13, 2002) thus includes the latest substitution matrices for
proteins (e. g. WAG), but unfortunately is slow when constructing trees.

Best wishes,



Dr. Kerstin Hoef-Emden=09=09=09Gyrhofstr. 15
Universit=E4t zu K=F6ln=09=09=0950931 K=F6ln
Botanisches Institut=09=09=09Germany

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