BEAST: Bayesian evolutionary analysis by sampling trees

01965 - 2 - Bayesian Evolutionary Analysis with BEAST

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed packag...

Sampling trees from evolutionary models.

A wide range of evolutionary models for species-level (and higher) diversification have been developed. These models can be used to test evolutionary hypotheses and provide comparisons with phylogenetic trees constructed from real data. To carry out these tests and comparisons, it is often necessary to sample, or simulate, trees from the evolutionary models. Sampling trees from these models is ...

A Note on Evolutionary Rate Estimation in Bayesian Evolutionary Analysis: Focus on Pathogens

Bayesian evolutionary analysis provide a statistically sound and flexible framework for estimation of evolutionary parameters. In this method, posterior estimates of evolutionary rate (μ) are derived by combining evolutionary information in the data with researcher’s prior knowledge about the true value of μ. Nucleotide sequence samples of fast evolving pathogens that are taken at d...

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogeneti...