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Perform pairwise sequence alignments

Bioconductor version: Release (3.19)

The two main functions in the package are pairwiseAlignment() and stringDist(). The former solves (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment problems. The latter computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.

Author: Patrick Aboyoun [aut], Robert Gentleman [aut], Hervé Pagès [cre]

Maintainer: Hervé Pagès <hpages.on.github at>

Citation (from within R, enter citation("pwalign")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Pairwise Sequence Alignments PDF R Script
Reference Manual PDF


biocViews Alignment, Genetics, SequenceMatching, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License Artistic-2.0
Depends BiocGenerics, S4Vectors, IRanges, Biostrings(>= 2.71.5)
Imports methods, utils
System Requirements
Bug Reports
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Suggests RUnit
Linking To S4Vectors, IRanges, XVector, Biostrings
Enhances Rmpi
Depends On Me amplican, hiReadsProcessor, iPAC, MethTargetedNGS, QSutils, R453Plus1Toolbox, sangeranalyseR, sangerseqR, CleanBSequences
Imports Me ChIPpeakAnno, ClustIRR, CNEr, crisprShiny, DominoEffect, enhancerHomologSearch, girafe, GUIDEseq, HTSeqGenie, IMMAN, IsoformSwitchAnalyzeR, LinTInd, methylscaper, motifbreakR, MSA2dist, openPrimeR, QuartPAC, scanMiR, ShortRead, SPLINTER, StructuralVariantAnnotation, svaNUMT, TFBSTools, XNAString, kmeRs
Suggests Me Biostrings, idpr, msa, RSVSim, dowser, seqtrie
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package pwalign_1.0.0.tar.gz
Windows Binary
macOS Binary (x86_64) pwalign_1.0.0.tgz
macOS Binary (arm64) pwalign_1.0.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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