pwalign
This is the development version of pwalign; for the stable release version, see pwalign.
Perform pairwise sequence alignments
Bioconductor version: Development (3.21)
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 "4.5") 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")| Pairwise Sequence Alignments | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Genetics, SequenceMatching, Sequencing, Software |
| Version | 1.3.0 |
| 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 |
See More
| Suggests | RUnit |
| Linking To | S4Vectors, IRanges, XVector, Biostrings |
| Enhances | Rmpi |
| Depends On Me | MethTargetedNGS, QSutils, R453Plus1Toolbox, amplican, hiReadsProcessor, sangeranalyseR, sangerseqR, CleanBSequences |
| Imports Me | CNEr, ChIPpeakAnno, ClustIRR, DominoEffect, GUIDEseq, IMMAN, IsoformSwitchAnalyzeR, LinTInd, MSA2dist, SPLINTER, ShortRead, StructuralVariantAnnotation, TFBSTools, XNAString, crisprShiny, enhancerHomologSearch, ggseqalign, girafe, methylscaper, motifbreakR, openPrimeR, scanMiR, svaNUMT, kmeRs |
| Suggests Me | BiocGenerics, Biostrings, RSVSim, idpr, msa, 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_1.3.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |