Msa: An R package for multiple sequence alignment

Ulrich Bodenhofer, Enrico Bonatesta, Christoph Horejš-Kainrath, Sepp Hochreiter

Research output: Contribution to journalArticlepeer-review

348 Citations (Scopus)


UNLABELLED: 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

Original languageEnglish
Pages (from-to)3997-3999
Number of pages3
Issue number24
Publication statusPublished - 3 Jul 2015
Externally publishedYes


  • Algorithms
  • Animals
  • Sequence Alignment/methods
  • Software


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