The program implements Smith-Waterman algorithm for performing local sequence alignment, finding similar regions between two nucleotide sequences. The approach is described in "Identification of Common Molecular Subsequences" , Journal of Molecular Biology, 147:195-197, 1981.The algorithm is a variation of the Needleman-Wunsch dynamic programming algorithm. It is guaranteed to find the optimal local alignment with respect to the scoring system being used (which includes the substitution matrix and the gap-scoring scheme).