Mathieu Fourment

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: PATRISTICv1.0 is a java program that calculates patristic distances from large trees in a range of file formats and allows graphical and statistical interpretation of distance matrices calculated by other programs and is used to analyse rates of mutation and substitutional saturation and the evolution of viruses.

TL;DR: Felsenstein's pruning algorithm is extended to allow efficient likelihood computations for models in which variation over branches (and not just sites) is described in the random effects likelihood framework, and this model treats the selective class of every branch at a particular site as an unobserved state that is chosen independently of that at any other branch.

TL;DR: It is concluded that the Y pestis lineages that caused the Plague of Justinian and the Black Death 800 years later were independent emergences from rodents into human beings.

TL;DR: The robustly estimated evolutionary rates spanned several orders of magnitude, from approximately 10−5 to 10−8 nucleotide substitutions per site year−1, and variation was negatively associated with sampling time, with this relationship best described by an exponential decay curve.