DOI: 10.18129/B9.bioc.msa    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see msa.

Multiple Sequence Alignment

Bioconductor version: 3.8

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>

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


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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:



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


biocViews Alignment, MultipleComparison, MultipleSequenceAlignment, Sequencing, Software
Version 1.14.0
In Bioconductor since BioC 3.1 (R-3.2) (4 years)
License GPL (>= 2)
Depends R (>= 3.1.0), methods, Biostrings(>= 2.40.0)
Imports Rcpp (>= 0.11.1), BiocGenerics, IRanges(>= 1.20.0), S4Vectors, tools
LinkingTo Rcpp
Suggests Biobase, knitr, seqinr, ape, phangorn
SystemRequirements GNU make
Depends On Me
Imports Me LymphoSeq, odseq
Suggests Me
Links To Me
Build Report  

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

Source Package msa_1.14.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) msa_1.14.0.tgz
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Source Repository (Developer Access) git clone
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