NOTE: these notes also apply to other installations, though the directories will be different.
This document and the example files hide in /home/nmra/gjb/amps. In order to run the programs you need to add the directory /home/nmra/gjb/bin to the path in your .cshrc file. Once this is done, typing
multalign will run multalign, and typing order will run the program order.
Any files referred to that are not in your working directory, must be given their FULL PATH NAMES. eg. the file md.mat is in /home/nmra/gjb/amps, so when specifying the matrix, the command is:
matrix_file=/home/nmra/gjb/amps/md.mat and NOT: matrix_file=ampsdir:md.mat or similar.
Running the program, eg. with the command file bash_look.com is achieved by simply typing
multalign < bash_look.com
The program may be run in batch using the "at" utility - see the manual page (ie type man at). To use at, you will need to create a simple shell script to run the program, for example, this might look like this:
multalign < bash_look.com > bash_look.log
or similar.
NOTE: amult program limits in this version are 500 sequences of up to 1200 residues.
Any queries, send e-mail with problem files to gjb@bioch.ox.ac.uk.