The msa package provides a unified R/Bioconductor interface to different multiple sequence alignment algorithms. Currently, ‘ClustalW’, ‘ClustalOmega’, and ‘MUSCLE’ are supported. All algorithms are usable without additional software packages and on all major platforms. The multiple sequence algorithms are complemented by an R interface to the powerful LaTeX package texshade.sty which allows for a highly customizable plots of multiple sequence alignments.
Enrico Bonatesta, Christoph Horejs-Kainrath, and Ulrich Bodenhofer <firstname.lastname@example.org>
U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015). msa: an R package for multiple sequence alignment. Bioinformatics 31(24):3997-3999. DOI: 10.1093/bioinformatics/btv494.
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