To cite aphylo in publications use the following paper:

Vega Yon G, Thomas D, Morrison J, Mi H, Thomas P, Marjoram P (2021). “Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees.” PLOS Computational Biology, 17, 1-35. ISSN 1367-4803, doi:10.1371/journal.pcbi.1007948, https://doi.org/10.1371/journal.pcbi.1007948.

And the actual R package:

Vega Yon G (2022). Statistical Inference of Annotated Phylogenetic Trees. R package version 0.3-2, https://github.com/USCBiostats/aphylo.

Corresponding BibTeX entries:

  @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},
  }

  @Manual{,
    title = {{{Statistical Inference of Annotated Phylogenetic
      Trees}}},
    author = {George {Vega Yon}},
    year = {2022},
    note = {R package version 0.3-2},
    url = {https://github.com/USCBiostats/aphylo},
  }