ProtML in molphy-2.3b3

Daniel Leonard leonard at datura.BCH.UMontreal.CA
Wed Sep 6 10:47:50 EST 2000

I have been testing protml in molphy-2.3b3.

I found out that the protml version in 2.3 seems broken. By running
exactly the same test on both versions (2.2 and 2.3b3), 2.3 segfaults.

By examining the core dump with gdb:
(gdb) backtrace
#0  0x31394 in pstree ()
#1  0x36584 in pml ()
#2  0x35518 in main ()

we can see that something happens in pstree(). With 2.2, the output seems

The test:

In gde, I selected some data then feed them to the following pipeline
(unlerlying a menuitem):

itemmethod:(mkdir ./Protml.$$; cd ./Protml.$$; readseq -a -f12 ../in1 |
sed 's/\~/-/g' > infile; protml -e -I infile > usertrees; protml -I infile
usertrees > outfile; /bin/rm -f ../in1; textedit outfile)&

protml dies in the second call "protml -I infile usertrees > outfile"

I have not been able to find any contact adresses of the authors.

Has it happen to anyone ?

Daniel Léonard

OGMP Informatics Division    E-Mail: leonard at bch.umontreal.ca
Département de Biochimie     Tel   : (514) 343-6111 ext 5149
Université de Montréal       Fax   : (514) 343-2210
Montréal, Quebec             Office: Pavillon Principal G-312
Canada H3C 3J7               WWW   :

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