BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
Remco R. Bouckaert,Joseph Heled,Denise Kühnert,Timothy G. Vaughan,Chieh-Hsi Wu,Dong Xie,Marc A. Suchard,Andrew Rambaut,Alexei J. Drummond +8 more
TLDR
BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform.Abstract:
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 package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.read more
Citations
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Journal ArticleDOI
ModelFinder: fast model selection for accurate phylogenetic estimates
Subha Kalyaanamoorthy,Subha Kalyaanamoorthy,Bui Quang Minh,Thomas K. F. Wong,Thomas K. F. Wong,Arndt von Haeseler,Arndt von Haeseler,Lars S. Jermiin,Lars S. Jermiin +8 more
TL;DR: ModelFinder is presented, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
Journal ArticleDOI
Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.
TL;DR: The software package Tracer is presented, for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference, which provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more.
Journal ArticleDOI
ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
TL;DR: An r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees, which can read more tree file formats than other softwares, and support visualization of phylo, multiphylo, phylo4, phyla4d, obkdata and phyloseq tree objects defined in other r packages.
Journal ArticleDOI
RDP4: Detection and analysis of recombination patterns in virus genomes.
TL;DR: The key feature of RDP4 that differentiates it from other recombination detection tools is its flexibility, which can be run either in fully automated mode from the command line interface or with a graphically rich user interface that enables detailed exploration of both individual recombination events and overall recombination patterns.
Journal ArticleDOI
Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10
TL;DR: The BEAST software package unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using Markov chain Monte Carlo integration.
References
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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
TL;DR: Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
Journal ArticleDOI
Evolutionary trees from DNA sequences: A maximum likelihood approach
TL;DR: A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available that allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests.
Journal ArticleDOI
BEAST: Bayesian evolutionary analysis by sampling trees
TL;DR: BEAST is a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree that provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions.
Journal ArticleDOI
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
Koichiro Tamura,Masatoshi Nei +1 more
TL;DR: In this paper, a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide substitutions was proposed, taking into account excess transitions, unequal nucleotide frequencies, and variation of substitution rate among different sites.
Journal ArticleDOI
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
TL;DR: The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7 is presented, which implements a family of Markov chain Monte Carlo algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses.
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