Aligns two sequences using the affine gap metric, a gap open penalty and a gap extension penalty. This method uses the existing gap open and extension penalties and similarity matrix. Set these using GapOpenCost, GapExtensionCost and SimilarityMatrix properties before calling this method.

Aligns two sequences using the affine gap metric, a gap open penalty and a gap extension penalty. This method uses the existing gap open and extension penalties and similarity matrix. Set these using GapOpenCost, GapExtensionCost and SimilarityMatrix properties before calling this method.

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