Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.
To see what versions of Exonerate are available type
module avail exonerate
To see what other modules are needed, what commands are available and how to get additional help type
module help exonerate
To use Exonerate, include a command like this in your batch script or interactive session to load the Exonerate module:
module load exonerate
Be sure to also load any other modules needed, as listed by the
module help exonerate command.