Aligns two sequences using a linear gap parameter, using existing gap open cost and similarity matrix. Set these using GapOpenCost and SimilarityMatrix properties before calling this method.

Aligns two sequences using a linear gap parameter, using existing gap open cost and similarity matrix. Set these using GapOpenCost and SimilarityMatrix properties before calling this method.

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.