BioPerl is a set of open source Perl modules designed expressly for manipulating molecular sequence data.  It comes as a part of the Rocks Bio Roll and is available on all HPC nodes.

Using BioPerl on HPC 

The BioPerl modules are especially helpful for pipelining multiple bininformatics analyses, parsing output, and interpreting results. The Rocks Bio Roll documentation is characteristically brief; much more information is available through the BioPerl home page. In particular see the HOWTOs, step-by-step tutorials of common bioinformatics tasks.  The modules are installed on the HPC in:

/opt/rocks/lib/perl5/site_perl/5.8.8/Bio