BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference
Guy Baele, Xiang Ji, Gabriel W. Hassler, John T. McCrone, Yucai Shao, Zhenyu Zhang, Andrew J. Holbrook, Philippe Lemey, Alexei J. Drummond, Andrew Rambaut, Marc A. Suchard
Abstract
Here we present the open-source and cross-platform BEAST X software that combines molecular phylogenetic reconstruction with complex trait evolution, divergence-time dating and coalescent demographics in an efficient statistical inference engine. BEAST X significantly advances the flexibility and scalability of evolutionary models supported. Novel clock and substitution models leverage a large variety of evolutionary processes; discrete, continuous and mixed traits with missingness and measurement errors; and fast, gradient-informed integration techniques that rapidly traverse high-dimensional parameter spaces.