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Bio.Alignment.SAlign

Contents

Smith-Waterman, or locally optimal alignment
Needleman-Wunsch, or globally optimal alignment

Description
Simple alignment of sequences Standard alignment/edit distance
Synopsis

local_score :: (Num a, Ord a) => SubstMx t a -> a -> Sequence t -> Sequence t -> a
local_align :: (Num a, Ord a) => SubstMx t a -> a -> Sequence t -> Sequence t -> EditList
global_score :: (Num a, Ord a) => SubstMx t a -> a -> Sequence t -> Sequence t -> a
global_align :: (Num a, Ord a) => SubstMx t a -> a -> Sequence t -> Sequence t -> EditList

Smith-Waterman, or locally optimal alignment

local_score :: (Num a, Ord a) => SubstMx t 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 -> Sequence t -> Sequence t -> EditList | Source

Needleman-Wunsch, or globally optimal alignment

global_score :: (Num a, Ord a) => SubstMx t 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 -> Sequence t -> Sequence t -> EditList | Source

Calculate alignments.
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