Bioinformatics perl script for virus identification

I need to proofread for best practice and optimize for speed, a bioinformatics script in perl/bioperl. And to write a CPAN script for installation on linux server. To use this script you will need: * Bioperl (L<http://www.bioperl.org/>) modules, * HMMER distribution (L<http://hmmer.janelia.org/>) and * FASTA distribution (L<ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/>).