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

And the actual R package:

Vega Yon G (2026). Statistical Inference of Annotated Phylogenetic Trees. R package version 0.3-6, 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 = {2026},
    note = {R package version 0.3-6},
    url = {https://github.com/USCBiostats/aphylo},
  }