BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. - Remco R. Bouckaert; Timothy G. Vaughan; Joëlle Barido-Sottani; Sebastián Duchêne; Mathieu Fourment; Alexandra Gavryushkina; Joseph Heled; Graham Jones; Denise Kühnert; Nicola De Maio; Michael Matschiner; Fábio K. Mendes; et al. (PLoS Comput. Biol., 2019)

CAFE 5 models variation in evolutionary rates among gene families. - Fábio K. Mendes; Dan Vanderpool; Ben Fulton; Matthew W. Hahn (Bioinform., 2021)

LinguaPhylo: A probabilistic model specification language for reproducible phylogenetic analyses. - Alexei J. Drummond; Kylie Chen; Fábio K. Mendes; Dong Xie (PLoS Comput. Biol., 2023)