How to score an alignment
Alignments are scored column by column. There is usually
a reward for character matches, a small penalty for
character mismatches, and a large penalty for gaps.
These penalties should be such that the highest scoring
alignment is the most likely one to reflect the true
evolutionary relationship of the loci. Two sequences can
be considered “similar” if their best alignment has a
sufficiently high score. The Smith-Waterman algorithm
finds the best scoring local alignment of two sequences of
length n and m respectively in running time O(n ·m).