AlignSimple aligns the set of input sequences using the linear gap model (one gap penalty), and returns the best alignment found.

AlignSimple aligns the set of input sequences using the linear gap model (one gap penalty), and returns the best alignment found.

Pairwise alignment of two sequences using a linear gap penalty. The various algorithms in derived classes (NeedlemanWunsch, SmithWaterman, and PairwiseOverlap) all use this general engine for alignment with a linear gap penalty.