To cite package 'msa' in publications use:

U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015) msa: an R package for multiple sequence alignment. Bioinformatics 31(24):3997-9999.<doi:10.1093/bioinformatics/btv176>.

If you use one of the three alignment algorithms, please cite the corresponding original paper. To obtain the reference in BibTex format, enter 'toBibtex(citation("msa"))'

Corresponding BibTeX entry:

  @Article{,
    title = {msa: an R package for multiple sequence alignment},
    author = {Ulrich Bodenhofer and Enrico Bonatesta and Christoph
      Horejs-Kainrath and Sepp Hochreiter},
    journal = {Bioinformatics},
    volume = {31},
    number = {24},
    pages = {3997--3999},
    year = {2015},
    doi = {10.1093/bioinformatics/btv494},
  }