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Bioconductor - pwalign (development version)

pwalign

This is the development version of pwalign; for the stable release version, see pwalign.

Perform pairwise sequence alignments

Bioconductor version: Development (3.22)

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] ORCID: 0009-0002-8272-4522

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

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

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details See More Suggests RUnit Linking To S4Vectors, IRanges, XVector, Biostrings Enhances Rmpi Depends On Me amplican, hiReadsProcessor, MethTargetedNGS, QSutils, R453Plus1Toolbox, sangeranalyseR, sangerseqR, CleanBSequences Imports Me ChIPpeakAnno, crisprShiny, DominoEffect, enhancerHomologSearch, ggseqalign, GUIDEseq, IMMAN, IsoformSwitchAnalyzeR, LinTInd, methylscaper, motifbreakR, MSA2dist, scanMiR, ShortRead, SPLINTER, StructuralVariantAnnotation, svaNUMT, TFBSTools, AntibodyForests, BIGr Suggests Me BiocGenerics, Biostrings, idpr, msa, RSVSim, dowser, geneviewer, seqtrie Links To Me Build Report Build Report Package Archives

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

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