Currently, the best way to cite rhierbaps in publications is to use:

Cheng, Lu, Thomas R. Connor, Jukka Sirén, David M. Aanensen, and Jukka Corander. 2013. Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software. Molecular Biology and Evolution 30 (5): 1224–28.

Corresponding BibTeX entry:

  @Article{,
    title = {Hierarchical and spatially explicit clustering of {DNA}
      sequences with {BAPS} software},
    author = {Lu Cheng and Thomas R Connor and Jukka Siren and David M.
      Aanensen and Jukka Corander},
    journal = {Mol. Biol. Evol.},
    year = {2013},
    volume = {30},
    number = {5},
    pages = {1224--1228},
    url = {http://dx.doi.org/10.1093/molbev/mst028},
  }