msa: an R package for multiple sequence alignment

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 LATEX package TEXshade which allows for flexible and customizable plotting of multiple sequence alignments. Availability: msa is available via the Bioconductor project