pwalign

Perform pairwise sequence alignments

Bioconductor version: Release (3.20)

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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("pwalign")

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

Documentation

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

browseVignettes("pwalign")

Pairwise Sequence Alignments	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Genetics, SequenceMatching, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
License	Artistic-2.0
Depends	BiocGenerics, S4Vectors, IRanges, Biostrings(>= 2.71.5)
Imports	methods, utils
System Requirements
URL	https://bioconductor.org/packages/pwalign
Bug Reports	https://github.com/Bioconductor/pwalign/issues

Suggests	RUnit
Linking To	S4Vectors, IRanges, XVector, Biostrings
Enhances	Rmpi
Depends On Me	amplican, hiReadsProcessor, MethTargetedNGS, QSutils, R453Plus1Toolbox, sangeranalyseR, sangerseqR, CleanBSequences
Imports Me	ChIPpeakAnno, ClustIRR, CNEr, crisprShiny, DominoEffect, enhancerHomologSearch, ggseqalign, girafe, GUIDEseq, IMMAN, IsoformSwitchAnalyzeR, LinTInd, methylscaper, motifbreakR, MSA2dist, openPrimeR, scanMiR, ShortRead, SPLINTER, StructuralVariantAnnotation, svaNUMT, TFBSTools, XNAString, kmeRs
Suggests Me	BiocGenerics, Biostrings, idpr, msa, RSVSim, dowser, seqtrie
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	pwalign_1.2.0.tar.gz
Windows Binary (x86_64)	pwalign_1.2.0.zip
macOS Binary (x86_64)	pwalign_1.2.0.tgz
macOS Binary (arm64)	pwalign_1.1.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pwalign
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pwalign
Bioc Package Browser	https://code.bioconductor.org/browse/pwalign/
Package Short Url	https://bioconductor.org/packages/pwalign/
Package Downloads Report	Download Stats