When using aphylo, please cite the following paper:

  Vega Yon GG, Thomas DC, Morrison J, Mi H, Thomas PD, et al. (2021)
  Bayesian parameter estimation for automatic annotation of gene
  functions using observational data and phylogenetic trees. PLOS
  Computational Biology 17(2): e1007948.
  https://doi.org/10.1371/journal.pcbi.1007948

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees},
    author = {George {Vega Yon} and Duncan Thomas and John Morrison and Huaiyu Mi and Paul Thomas and Paul Marjoram},
    journal = {PLOS Computational Biology},
    year = {2021},
    month = {feb},
    volume = {17},
    issue = {2},
    doi = {10.1371/journal.pcbi.1007948},
    url = {https://doi.org/10.1371/journal.pcbi.1007948},
    issn = {1367-4803},
    pages = {1-35},
  }

And the actual R package:

  Vega Yon G (????). _Statistical Inference of Annotated Phylogenetic
  Trees_. R package version 0.3-4,
  <https://github.com/USCBiostats/aphylo>.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {{{Statistical Inference of Annotated Phylogenetic Trees}}},
    author = {George {Vega Yon}},
    note = {R package version 0.3-4},
    url = {https://github.com/USCBiostats/aphylo},
  }