Align aligns the set of input sequences using the affine gap model (gap open and gap extension penalties) and returns the best alignment found.

A convenience method - we know there are exactly two inputs. Align uses the affine gap model, which requires a gap open and a gap extension penalty.

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

A convenience method - we know there are exactly two inputs. AlignSimple uses a single gap penalty.