 The PairWise algorithm is a variant of the Smith–Waterman algorithm best local alignment algorithm.These algorithms all belong to the class known as minimal string edit algorithms.The main differences between PairWise and other alignment algorithm is that, besides normal penalties such as Gap Opening Penalty (GOP), Gap Extension Penalty (GEP) and Match, PairWise introduced two new penalties called Frame Opening Penalty (FOP) and Frame Extension Penalty (FEP), which will be incurred when a frameshift is accepted and extended respectively.