1. Set ISPALIGN_DIR in src/default.h to the absolute path in which the ispalign 
   directory is located.

2. Type ./install to install ispalign.

3. The executable file ispalign is in bin.  Either move it to a directory on
   the search path or add the directory bin to the search path.

4. Execute ispalign with the command

         bin/ispalign 1aboA_ref1.pep

   where 1aboA_ref1.pep is a fasta input file included as an example.  Core
   dumps from this step can be ignored.  The alignment will still be produced
   correctly.

   The current version of ispalign accepts one argument specifying the input
   file in fasta format.  The output alignment will be put into a file with
   extension .aln added to the filename.

More information on ispalign is available at http://faculty.cs.tamu.edu/shsze.