Using Perl for sequence alignment? Oof, I did not expect to be blindsided with such an incredibly esoteric flashback to one bioinformatics class many years ago

Using Perl for sequence alignment? Oof, I did not expect to be blindsided with such an incredibly esoteric flashback to one bioinformatics class many years ago. I eventually ended up rewriting the thing into an excessive Java/Swing program which animated its work through all the comparisons, showing show best paths and dead-ends. It involved a BLOSUM64 matrix, so I must've been aligning based on what amino acids were being coded-for, even if underlying base pairs differed.