The program is run from a command file that contains a series of keyword commands that tell the program which files to use for what, how to format the output and above all, which type of alignment to perform.
Keyword commands are all followed by an equals sign '=' which may in turn be followed by a string of arguments in free format. The precise formats for each command are described in APPENDIX 1. Keyword commands may be in upper or lower case or mixed case. See APPENDIX 2 for a full description of input/output file formats.
NOTE: All filenames must be fully qualified. The examples shown in this manual give filenames as e.g. ``ampsdir:md.mat'', you need to change this to indicate the exact path for the file, e.g. ``/home/geoff/gjb/md/md.mat'', or wherever the file is on your computer system.
Once you have created the command file, for example ``test.com'', then run multalign by typing:
multalign < test.com
All results and error messages will be written to the output file, so look here to see if all has worked well.