Registration Open for Bioc2024 July 24-26


Multiple Sequence Alignment

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") 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 1.36.0
In Bioconductor since BioC 3.1 (R-3.2) (9.5 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
See More
Suggests Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign
Linking To Rcpp
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_1.36.0.tar.gz
Windows Binary
macOS Binary (x86_64) msa_1.36.0.tgz
macOS Binary (arm64) msa_1.36.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats