bio-0.4.6: A bioinformatics librarySource codeContentsIndex
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 -> aSource
Calculate local edit distance (Smith-Waterman alignment score)
local_align :: (Num a, Ord a) => SubstMx t a -> a -> Sequence t -> Sequence t -> EditListSource
Needleman-Wunsch, or globally optimal alignment
global_score :: (Num a, Ord a) => SubstMx t a -> a -> Sequence t -> Sequence t -> aSource
Calculate global edit distance (Needleman-Wunsch alignment score)
global_align :: (Num a, Ord a) => SubstMx t a -> a -> Sequence t -> Sequence t -> EditListSource
Calculate alignments.
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