title: msa: an R package for multiple sequence alignment.
abstract: 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.
  
  
  METHODS
  msa is available via the Bioconductor project: http://bioconductor.org/packages/release/bioc/html/msa.html. Further information and the R code of the example presented in this paper are available at http://www.bioinf.jku.at/software/msa/.
authors: Institute of Bioinformatics, Johannes Kepler University, Linz, Austria.
authors: Ulrich
authors: U
authors: Bodenhofer
authors: Institute of Bioinformatics, Johannes Kepler University, Linz, Austria.
authors: Enrico
authors: E
authors: Bonatesta
authors: Institute of Bioinformatics, Johannes Kepler University, Linz, Austria.
authors: Christoph
authors: C
authors: Horejš-Kainrath
authors: Institute of Bioinformatics, Johannes Kepler University, Linz, Austria.
authors: Sepp
authors: S
authors: Hochreiter
mesh_terms: D000465:Algorithms; D000818:Animals; D016415:Sequence Alignment / Q000379:methods*; D012984:Software