Bio.Alignment.AAlign
 Contents Smith-Waterman, or locally optimal alignment with affine gaps Needleman-Wunsch, or globally optimal alignment with affine gaps
Description

Implement alignments/edit distance with affine gap penalties

I've seen g = (-10,-1) as the suggested price to pay for a gaps using BLOSUM62. Good choice as any, I guess.

Synopsis
 local_score :: (Num a, Ord a) => SubstMx t a -> (a, a) -> Sequence t -> Sequence t -> a local_align :: (Num a, Ord a) => SubstMx t a -> (a, a) -> Sequence t -> Sequence t -> (a, EditList) global_score :: (Num a, Ord a) => SubstMx t a -> (a, a) -> Sequence t -> Sequence t -> a global_align :: (Num a, Ord a) => SubstMx t a -> (a, a) -> Sequence t -> Sequence t -> (a, EditList)
Smith-Waterman, or locally optimal alignment with affine gaps
 local_score :: (Num a, Ord a) => SubstMx t a -> (a, a) -> Sequence t -> Sequence t -> a Source
Calculate local edit distance (Smith-Waterman alignment score)
 local_align :: (Num a, Ord a) => SubstMx t a -> (a, a) -> Sequence t -> Sequence t -> (a, EditList) Source
Calculate local alignmnet (Smith-Waterman)
Needleman-Wunsch, or globally optimal alignment with affine gaps
 global_score :: (Num a, Ord a) => SubstMx t a -> (a, a) -> Sequence t -> Sequence t -> a Source
Calculate global edit distance (Needleman-Wunsch alignment score)
 global_align :: (Num a, Ord a) => SubstMx t a -> (a, a) -> Sequence t -> Sequence t -> (a, EditList) Source
Calculate global alignment (Needleman-Wunsch)