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msa

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

Multiple Sequence Alignment


Bioconductor version: Development (3.20)

The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.

Author: Enrico Bonatesta [aut], Christoph Kainrath [aut], Ulrich Bodenhofer [aut,cre]

Maintainer: Ulrich Bodenhofer <ulrich at bodenhofer.com>

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

Installation

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


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

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

BiocManager::install("msa")

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("msa")
msa - An R Package for Multiple Sequence Alignment PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, MultipleComparison, MultipleSequenceAlignment, Sequencing, Software
Version 1.37.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License GPL (>= 2)
Depends R (>= 3.3.0), methods, Biostrings(>= 2.40.0)
Imports Rcpp (>= 0.11.1), BiocGenerics, IRanges(>= 1.20.0), S4Vectors, tools
System Requirements GNU make
URL https://github.com/UBod/msa
See More
Suggests Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign
Linking To Rcpp
Enhances
Depends On Me
Imports Me LymphoSeq, odseq, surfaltr, SeedMatchR
Suggests Me idpr, bio3d, datelife
Links To Me
Build Report Build Report

Package Archives

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

Source Package msa_1.37.0.tar.gz
Windows Binary msa_1.37.0.zip
macOS Binary (x86_64) msa_1.37.0.tgz
macOS Binary (arm64) msa_1.37.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/msa
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/msa
Bioc Package Browser https://code.bioconductor.org/browse/msa/
Package Short Url https://bioconductor.org/packages/msa/
Package Downloads Report Download Stats