F. K. Mendes

How to validate a Bayesian evolutionary model

This paper describes good practices for validating Bayesian models in computational biology and introduces tools to automate validation protocols.

LinguaPhylo: a probabilistic model specification language for reproducible phylogenetic analyses

This paper introduces a new model specification language, LPhy, for phylogenetic analyses to improve reproducibility and clarity in model descriptions.

Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales

This paper introduces a new evolutionary model, FBD-MSC, that integrates genealogical and fossilization processes to improve divergence time estimates in Caninae.

BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis

The paper describes new developments in the BEAST 2.5 software platform for Bayesian evolutionary analysis, expanding joint inference over multiple data types and complex phylodynamics.

The perils of intralocus recombination for inferences of molecular convergence

The paper examines how intralocus recombination leads to false convergence inferences (hemiplasy) when analyzing molecular data from single loci in primates and Drosophila.

Why concatenation fails in the anomaly zone

The paper shows that likelihood-based methods fail to recover species trees from concatenated data in and near the anomaly zone, while maximum-parsimony succeeds.