Msa: an R package for multiple sequence alignment. (26th August 2015)

• Record Type: Journal Article
• Authors: Bodenhofer, Ulrich; Bonatesta, Enrico; Horejš-Kainrath, Christoph; Hochreiter, Sepp
• Is Part Of: Bioinformatics. Volume 31:Number 24(2015)
• Page Start: 3997
• Page End: 3999
• Publication Date: 2015-08-26
• Subjects: Bioinformatics -- Periodicals; Genomics -- Data processing -- Periodicals; Computational biology -- Periodicals; 572.80285
• DOI: 10.1093/bioinformatics/btv494
• Languages: English
• ISSNs: 1367-4803

Abstract

Abstract : 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: [e-mail] or [e-mail]