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.

A BibTeX entry for LaTeX users is

  @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},
  }

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"))'