ProtML in molphy-2.3b3

Russell Malmberg russell at dogwood.botany.uga.edu
Thu Sep 7 08:58:27 EST 2000


I've had better luck with 2.3b3 converting the input data files to the 
unique molphy format first, then not using the -I option.  They have a perl 
script in the distribution that will convert from phylip to molphy.

Even so, I've only been able to get 2.3b3 to work on UNIX machines, not on 
Win32, where I get similar memory errors under any condition.

Russell

-- 

 Russell L. Malmberg
 russell at dogwood.botany.uga.edu
 http://www.botany.uga.edu/malmberg


leonard at datura.BCH.UMontreal.CA (Daniel Leonard) wrote in 
<Pine.GSO.4.21.0009061115300.14518-100000 at datura.BCH.UMontreal.CA>:

>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
>OK.
>
>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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