The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.
This is the source code repository. The package can be installed from Bioconductor. Further information and installation instructions are also available from http://www.bioinf.jku.at/software/msa/.
Although the package is maintained by Ulrich Bodenhofer, the package itself has been implemented mainly by Enrico Bonatesta and Christoph Kainrath-Horejs.