When using aphylo, please cite the following paper:

Vega Yon GG, Thomas DC, Morrison J, Mi H, Thomas PD, Marjoram P (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 R package itself:

Vega Yon G (2026). aphylo: Statistical Inference and Prediction of Annotations in Phylogenetic Trees. doi:10.32614/CRAN.package.aphylo. 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},
    number = {2},
    pages = {e1007948},
    issn = {1553-7358},
    doi = {10.1371/journal.pcbi.1007948},
    url = {https://doi.org/10.1371/journal.pcbi.1007948},
  }

  @Manual{,
    title = {{{aphylo: Statistical Inference and Prediction of
      Annotations in Phylogenetic Trees}}},
    author = {George {Vega Yon}},
    year = {2026},
    note = {R package version 0.3-6},
    url = {https://github.com/USCbiostats/aphylo},
    doi = {10.32614/CRAN.package.aphylo},
  }