Joëlle Barido-Sottani

TL;DR: A series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release are described.

TL;DR: The full range of new tools and models available on the BEAST 2.5 platform are described, which expand joint evolutionary inference in many new directions, especially for joint inference over multiple data types, non-tree models and complex phylodynamics.

TL;DR: There is a need for more readily available resources aimed at helping interested scientists equip themselves with the skills to confidently use cutting-edge phylogenetic analysis software, and here, the “Taming the Beast” resource is introduced, to facilitate the usage of the Bayesian phylogenetic software package BEAST 2.

TL;DR: A comparison of alternative approaches for handling fossil age uncertainty in analysis using the FBD process finds that fixing fossil ages to the midpoint or a random point drawn from within the stratigraphic age range leads to biases in divergence time estimates, while sampling fossil ages leads to estimates that are similar to inferences that employ the correct ages of fossils.

TL;DR: A new multitype birth–death model (MTBD) that can estimate lineage-specific birth and death rates for species phylogenies, and lineage-dependent transmission and recovery rates for pathogen transmission trees is presented.