To cite the package 'MonoPhy' in publications use:

Schwery O, O'Meara B (2016). “MonoPhy: a simple R package to find and visualize monophyly issues.” PeerJ Computer Science, 2, e56. ISSN 2376-5992, doi: 10.7717/peerj-cs.56, https://doi.org/10.7717/peerj-cs.56.

You may also want to cite the version number you used (found via 'library(help=MonoPhy)').

Corresponding BibTeX entry:

  @Article{,
    title = {MonoPhy: a simple R package to find and visualize
      monophyly issues},
    author = {Orlando Schwery and Brian C. O'Meara},
    year = {2016},
    volume = {2},
    pages = {e56},
    journal = {PeerJ Computer Science},
    issn = {2376-5992},
    url = {https://doi.org/10.7717/peerj-cs.56},
    doi = {10.7717/peerj-cs.56},
  }