I don't know, but then, I'm not actually fluent in the terms of biology and computations relating to that. What did the Google search for alignment on this site tell you and how are the solutions/discussions there not helping?

If they are not helping, maybe you can explain to us what your data structure is, and what an alignment is and how one alignment would be preferrable over another alignment.

I guess you've looked at BioPerl already and found none of its methods sufficient for your task?