A topology-marginal composite likelihood via a generalized phylogenetic pruning algorithm

Automatic Differentiation is no Panacea for Phylogenetic Gradient Computation

(2023) Mathieu Fourment et al.   Genome Biology and Evolution

Gradients do grow on trees: a linear-time 𝒪 (N)-dimensional gradient for statistical phylogenetics

(2020) Xiang Ji et al.   MOLECULAR BIOLOGY AND EVOLUTION

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics

(2019) Daniel L Ayres et al.   SYSTEMATIC BIOLOGY

19 Dubious Ways to Compute the Marginal Likelihood of a Phylogenetic Tree Topology

(2019) Mathieu Fourment et al.   SYSTEMATIC BIOLOGY

Virus genomes reveal factors that spread and sustained the Ebola epidemic

(2017) Gytis Dudas et al.   NATURE

Quantifying MCMC Exploration of Phylogenetic Tree Space

(2015) Chris Whidden et al.   SYSTEMATIC BIOLOGY

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Estimation of Tree Posterior Probabilities Using Conditional Clade Probability Distributions

(2013) Bret Larget   SYSTEMATIC BIOLOGY

Hessian Calculation for Phylogenetic Likelihood based on the Pruning Algorithm and its Applications

(2012) Toby Kenney et al.   Statistical Applications in Genetics and Molecular Biology

Guided Tree Topology Proposals for Bayesian Phylogenetic Inference

(2011) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes

(2011) Maria Anisimova et al.   SYSTEMATIC BIOLOGY

Signal and Image Processing with Belief Propagation [DSP Applications]

(2008)   IEEE SIGNAL PROCESSING MAGAZINE

Efficiency of Markov Chain Monte Carlo Tree Proposals in Bayesian Phylogenetics

(2008) Clemens Lakner et al.   SYSTEMATIC BIOLOGY