Bayesian Phylogenetics with BEAUti and the BEAST 1.7

By Alexei J. Drummond, Marc A. Suchard, Dong Xie, Andrew Rambaut. Molecular biology and evolution, 2012

1,674 citations recorded by the source corpus.

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 phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/892615c04e07d3087c2a727a28d42d7caffaade8

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Citations in the corpus

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 (2018, methodology): “Tracer works automatically with sample output from BEAST (Drummond et al. 2012), BEAST2 (Bouckaert et al.”
Biogeographical diversification of mainland Asian Dendrobium (Orchidaceae) and its implications for the historical dynamics of evergreen broad‐leaved forests (2016, neutral): “The maximum clade credibility tree was computed using treeAnnotator 1.7.4 (Drummond et al., 2012).”
SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes. (2016, background): “A typical SpreaD3 analysis proceeds in two steps: The first step consists in parsing and analyzing the BEAST output in order to create a data file conforming to Java Script Object Notation (JSON) format.”
Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) (2016, neutral): “Time-scaled trees can be estimated using many statistical approaches, including Bayesian inference (e.g., Drummond et al. 2012), maximum likelihood (e.g., Rambaut 2000; Sanderson 2003; Yang 2007), or heuristic methods (e.g., Drummond and Rodrigo 2000).”
Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 (2018, background): “…Analysis by Sampling Trees (BEAST) software package has become firmly established in a broad diversity of biological fields from phylogenetics and paleontology, population dynamics, ancient DNA, and the phylodynamics and molecular epidemiology of infectious disease (Drummond et al. 2012).”
Ultrafast Approximation for Phylogenetic Bootstrap (2013, methodology): “Bayesian MCMC methods, however, tend to overestimate the true probabilities in case of model misspeciﬁcation or polytomies (Suzuki et al. 2002; Douady et al. 2003; Lewis et al. 2005; Anisimova et al. 2011).”
Into the light: diurnality has evolved multiple times in geckos (2015, methodology): “We estimated phylogenetic relationships and divergence times simultaneously in a Bayesian framework using BEAST 1.7.4 (Drummond et al., 2012).”
Global circulation patterns of seasonal influenza viruses vary with antigenic drift (2015, neutral): “8.1 25 and incorporated the SRD06 nucleotide substitution model 26 , a coalescent demographic model with constant effective population size and a strict molecular clock across branches.”
Fast Dating Using Least-Squares Criteria and Algorithms (2015, neutral): “Some programs (e.g., PAML, Rannala and Yang 2007) perform calculations on a fixed, user-supplied tree, while others (e.g., BEAST, Drummond and Rambaut 2007; Drummond et al. 2012) infer the tree from the sequence alignment.”
Integrating influenza antigenic dynamics with molecular evolution (2013, methodology): “Source code implementing the cartographic models has been made fully available as part of the software package BEAST [28], and can be downloaded from its Google code repository (http://code.google.com/p/beast-mcmc/).”