pwalign
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 gmail.com>
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 | R Script | |
Reference Manual | ||
NEWS | Text |
Details
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 | |
URL | https://bioconductor.org/packages/pwalign |
Bug Reports | https://github.com/Bioconductor/pwalign/issues |
See More
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 | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | pwalign_1.0.0.tar.gz |
Windows Binary | pwalign_1.0.0.zip |
macOS Binary (x86_64) | pwalign_1.0.0.tgz |
macOS Binary (arm64) | pwalign_1.0.0.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 |