msa: an R package for multiple sequence alignment

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 al...

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Published inBioinformatics (Oxford, England) Vol. 31; no. 24; pp. 3997 - 3999
Main Authors Bodenhofer, Ulrich, Bonatesta, Enrico, Horejš-Kainrath, Christoph, Hochreiter, Sepp
Format Journal Article
LanguageEnglish
Published England 15.12.2015
Subjects
Algorithms
Animals
Sequence Alignment - methods
Software
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Summary: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: 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/. Contact:  bodenhofer@bioinf.jku.at or msa@bioinf.jku.at
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ISSN:1367-4803
1367-4811
1367-4811
DOI:10.1093/bioinformatics/btv494