== NOTES == Having an alignment matrix is obsolete. The code for dealing with the worst case problem (which would almost never happen in biological data), i.e. when the the other sequence has nothing in common with the first, is hidden in print_alignment()—notice, that there is no "elseif alignments[x, y] == XY" but an "else", so the two alignment string in the worst case are the strings themselves + neccesarry gaps, so the initial alignment should be just that. We should propose a new alignment string (one gapped string for each sequence) in the main loop, and update that if it is better.