Statistical Inference and Prediction of Annotations in Phylogenetic Trees R package aphylo version 0.3-6 Classification/MSC: 90C35, 90B18, 91D30 Implements a parsimonious evolutionary model to analyze and predict gene-functional annotations in phylogenetic trees as described in Vega Yon et al. (2021) <doi:10.1371/journal.pcbi.1007948>. Focusing on computational efficiency, 'aphylo' makes it possible to estimate pooled phylogenetic models, including thousands (hundreds) of annotations (trees) in the same run. The package also provides the tools for visualization of annotated phylogenies, calculation of posterior probabilities (prediction) and goodness-of-fit assessment featured in Vega Yon et al. (2021). Software Depends: R (>= 3.5.0), ape (>= 5.0) Imports: Rcpp (>= 0.12.1), Matrix, methods, coda, fmcmc, utils, MASS, xml2 LinkingTo: Rcpp Suggests: covr, knitr, tinytest, AUC, rmarkdown, George Vega Yon <g.vegayon@gmail.com> Comprehensive R Archive Network (CRAN) George Vega Yon [aut, cre] (ORCID: <https://orcid.org/0000-0002-3171-0844>), National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02), USC Biostatistics [cph] MIT + file LICENSE (https://CRAN.R-project.org/package=aphylo/LICENSE) 2026-01-09 application/tgz https://CRAN.R-project.org/package=aphylo doi:10.32614/CRAN.package.aphylo