msa

DOI: 10.18129/B9.bioc.msa  

Multiple Sequence Alignment

Bioconductor version: Release (3.16)

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, Christoph Horejs-Kainrath, Ulrich Bodenhofer

Maintainer: Ulrich Bodenhofer <bodenhofer at bioinf.jku.at>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

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

Details

biocViews	Alignment, MultipleComparison, MultipleSequenceAlignment, Sequencing, Software
Version	1.30.1
In Bioconductor since	BioC 3.1 (R-3.2) (8 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
LinkingTo	Rcpp
Suggests	Biobase, knitr, seqinr, ape (>= 5.1), phangorn
SystemRequirements	GNU make
Enhances
URL	http://www.bioinf.jku.at/software/msa/
Depends On Me
Imports Me	LymphoSeq, odseq, surfaltr
Suggests Me	idpr
Links To Me
Build Report

Package Archives

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

Source Package	msa_1.30.1.tar.gz
Windows Binary	msa_1.30.1.zip
macOS Binary (x86_64)	msa_1.30.1.tgz
macOS Binary (arm64)	msa_1.30.1.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
Old Source Packages for BioC 3.16	Source Archive