## README

# smith-waterman algorithm

implementation of smith-waterman algorithm, as described here and here. signature of the only exported method is *(seq1, seq2, gss, simfunc)*. seq1 and seq2 are sequence 1 and sequence 2 (must be arrays or strings). gss is gap scoring scheme - a function, which, given a deletion/insertion gap distance would produce a penalty score for that distance. its signature is *(k)*, where k is gap distance. simfunc is similarity function, which would produce a score for given symbols in sequence 1 and sequence 2. its signature is *(symb1, symb2)*, where symb1 is symbol from sequence 1 and symb2 is symbol from sequence 2. check your arguments before invoking it!