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Multiple Sequence Alignment

Bioconductor version: Release (3.18)

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>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Alignment, MultipleComparison, MultipleSequenceAlignment, Sequencing, Software
Version 1.34.0
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 http://www.bioinf.jku.at/software/msa/
See More
Suggests Biobase, knitr, seqinr, ape (>= 5.1), phangorn
Linking To Rcpp
Depends On Me
Imports Me LymphoSeq, odseq, surfaltr
Suggests Me idpr
Links To Me
Build Report Build Report

Package Archives

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

Source Package msa_1.34.0.tar.gz
Windows Binary msa_1.34.0.zip
macOS Binary (x86_64) msa_1.34.0.tgz
macOS Binary (arm64) msa_1.34.0.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