Local Sequence Alignment Against a Database Problem

Implementation of the algorithms set out in https://users.csc.calpoly.edu/~dekhtyar/448-Spring2013/lectures/lec08.448.pdf for the following problem:

Given two strings S = s1 . . . sn and T = t1 . . . tm, a substitution matrix Score and an insertion/deletion penalty δ, find a pair of substrings si . . . si+k of S and tj . . . tj+l of T that have the best overall alignment score, and return the best alignment for them.