pwalign

Perform pairwise sequence alignments

Bioconductor version: 3.23 · Package version: 1.8.0

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.

Installation

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

BiocManager::install("pwalign")

Details

Maintainer	Hervé Pagès <hpages.on.github@gmail.com>
Author	Patrick Aboyoun [aut], Robert Gentleman [aut], Hervé Pagès [cre] (ORCID: <https://orcid.org/0009-0002-8272-4522>)
License	Artistic-2.0
URL	https://bioconductor.org/packages/pwalign
Bug Reports	https://github.com/Bioconductor/pwalign/issues
Downloads rank	8726
Source branch	RELEASE_3_23
biocViews	Alignment, Genetics, SequenceMatching, Sequencing, Software

Documentation

Pairwise Sequence Alignments

Download

Source package

Dependencies

Depends: BiocGenerics, S4Vectors, IRanges, Biostrings (>= 2.71.5)

Imports: methods, utils

LinkingTo: S4Vectors, IRanges, XVector, Biostrings

Suggests: RUnit

Enhances: Rmpi

Reverse dependencies

Depends On Me (7): amplican, CleanBSequences, MethTargetedNGS, QSutils, R453Plus1Toolbox, sangeranalyseR, sangerseqR

Imports Me (31): AbSolution, AntibodyForests, BIGr, ChIPpeakAnno, chromVAR, CNEr, crisprShiny, DiPALM, DominoEffect, dowser, enhancerHomologSearch, ggseqalign, GUIDEseq, IMMAN, IsoformSwitchAnalyzeR, longreadvqs, methylscaper, motifbreakR, MSA2dist, ogrdbstats, openPrimeR, PACVr, revert, scanMiR, scifer, ShortRead, SpliceImpactR, SPLINTER, StructuralVariantAnnotation, svaNUMT, TFBSTools

Suggests Me (8): BiocGenerics, Biostrings, geneviewer, idpr, msa, mutscan, RSVSim, seqtrie