msa: an R package for multiple sequence alignment

Bioinformatics. 2015 Dec 15;31(24):3997-9. doi: 10.1093/bioinformatics/btv494. Epub 2015 Aug 26.


Although the R platform and the add-on packages of the Bioconductor project are widely used in bioinformatics, the standard task of multiple sequence alignment has been neglected so far. The msa package, for the first time, provides a unified R interface to the popular multiple sequence alignment algorithms ClustalW, ClustalOmega and MUSCLE. The package requires no additional software and runs on all major platforms. Moreover, the msa package provides an R interface to the powerful package shade which allows for flexible and customizable plotting of multiple sequence alignments.

Availability and implementation: msa is available via the Bioconductor project: Further information and the R code of the example presented in this paper are available at

MeSH terms

  • Algorithms
  • Animals
  • Sequence Alignment / methods*
  • Software*