I'd suggest you post either some code here or a more detailed description of what your code acutally does. I have a suspicion that it is not a BioPerl problem but the design of the algorithm that makes it so slow. From your question I would guess that you are still learning Perl, right? One common beginner's mistake is to repeatedly read large sequence files where a single pass would have been sufficient. What are you using to compare the sequences? For example, if you are running something like ClustalW of all possible pairs of a large file of sequences then this will take forever. You could then speed this up by running a MEGABLAST or BLASTCLUST or something like that to first identify sequences with some similarity and then only do the global alignments for those where it makes sense. There is also a plethorea of new aligners for next-gen sequencing data out there, which could also be useful, depending on your data.