In <199403180105.AA15407 at wugate.wustl.edu> brett at BORCIM.WUSTL.EDU writes:
> 1- Find a program that can handle the number of sequences I want
> 2- Modify LINEUP to do the same.
We did the latter. I append a description on how to do it, posted by Rodrigo
Lopez of the Norwegian EMBnet Node about two weeks ago. As you run GCG under
VMS I modified the description accordingly.
By the way: you may wish to modify PileUp in the same manner.
Regards
Christoph Gartmann
Newsgroups: bionet.software.gcg
Subject: Re: Help on Lineup program
From: rodrigol at biomaster.uio.no (Rodrigo Lopez)
Date: 3 Mar 1994 09:12:31 GMT
> 1. make a copy of the lineup.for source in a directory of your own.
> 2. make a copy of the lineup.inc file in a directory of you own.
$ CREATE/DIRECTORY/PROT=(O:RWED) [.newlineup]
$ SET DEFAULT [.newlineup]
$ gcg
$ gcgsupport
$ COPY gensource:lineup.for []
$ COPY geninclude:lineup.inc []
> 3. Edit the lineup.inc file to reflect the following changes:
>> Parameter NAMELEN = 11
> >>>>> Parameter HighRow = 15, LowRow = -15
> Parameter MaxSeqs = 500
> Parameter MaxBuffs = 10
>> to
>> Parameter HighRow = 30, LowRow = -30 !depending on your needs
4. Edit LINEUP.FOR and replace all occurences of
Include 'GenInclude:LineUp.inc'
into
Include 'LineUp.inc'
5. Compile your modified Lineup
$ FORTRAN/EXTEND_SOURCE lineup.for ! line 2708 is longer than 72
6. Link the program
$ sharelink lineup
7. Run the program
$ newlineup :== $my_disk:[my_directory.newlineup]newlineup
$ newlineup
> Please remember that I'm assuming you don't have an exagerately big
> alignment and that the fragment length of each sequence must be
> kept 'small' (i.e. max 300 aa).
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