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

Cheng L, Connor TR, Siren J, Aanensen DM, Corander J (2013). “Hierarchical and spatially explicit clustering of DNA sequences with BAPS software.” Mol. Biol. Evol., 30(5), 1224–1228. http://dx.doi.org/10.1093/molbev/mst028.

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},
  }