When using aphylo, please cite 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 (2025).Statistical Inference of Annotated Phylogenetic Trees.R package version 0.3-5,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 = {2025}, note = {R package version 0.3-5}, url = {https://github.com/USCBiostats/aphylo}, }