On the importance of assessing topological convergence in Bayesian phylogenetic inference

no code implementations • 18 Feb 2024 • Marius Brusselmans, Luiz Max Carvalho, Samuel L. Hong, Jiansi Gao, Frederick A. Matsen IV, Andrew Rambaut, Philippe Lemey, Marc A. Suchard, Gytis Dudas, Guy Baele

Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distribution.

Gradients do grow on trees: a linear-time ${\cal O}\hspace{-0.2em}\left( N \right)$-dimensional gradient for statistical phylogenetics

1 code implementation • 29 May 2019 • Xiang Ji, Zhen-Yu Zhang, Andrew Holbrook, Akihiko Nishimura, Guy Baele, Andrew Rambaut, Philippe Lemey, Marc A. Suchard

To make this tractable, we present a linear-time algorithm for ${\cal O}\hspace{-0. 2em}\left( N \right)$-dimensional gradient evaluation and apply it to general continuous-time Markov processes of sequence substitution on a phylogenetic tree without a need to assume either stationarity or reversibility.

Computation Populations and Evolution Methodology

Spatio-temporal Dynamics of Foot-and-Mouth Disease Virus in South America

1 code implementation • 5 May 2015 • Luiz Max Carvalho, Nuno Rodrigues Faria, Andres M. Perez, Marc A. Suchard, Philippe Lemey, Waldemir de Castro Silveira, Andrew Rambaut, Guy Baele

Although foot-and-mouth disease virus (FMDV) incidence has decreased in South America over the last years, the pathogen still circulates in the region and the risk of re-emergence in previously FMDV-free areas is a veterinary public health concern.