BEAST Software - Bayesian Evolutionary Analysis Sampling Trees | BEAST Documentation_Travel & Tourism

Toggle navigation BEASTdoc Nav Contents FAQ Help Source Code News Contents Getting Started About Installing Introductory Tutorials Software Packages BEAUti, BEAST and other programs BEAGLE Library Tracer FigTree TempEst SPREAD SPREAD3 PiBUSS BEASTGen Tutorials First Tutorial Second Tutorial Rates and Dates Temporal Signal using TempEst Bayesian Evaluation of Temporal Signal Online phylodynamic inference Phylodynamics of an epidemic Phylodynamics of seasonal influenza Analysing Continuous Traits How-To Guides Create taxon sets Specify sampling dates Tip date sampling Construct a model in BEAUti Analyse BEAST output Convergence diagnostics in Tracer Summarize trees Create custom substitution models Create Markov-modulated models Advanced Tutorials Hierarchical Phylogenetic Model Tutorial Markov Jumps and Rewards Tutorial Adaptive MCMC Tutorial Model Selection Tutorial Model Selection Advanced Tutorial Model Selection Examples Clock Model Averaging Tutorial Epoch Model Tutorial Time-Dependent Rate Model Tutorial Phylogeography with individual travel history Analysing datasets with tens of thousands of taxa Workshop Tutorials Estimating Rates and Dates Evolutionary Dynamics of Influenza Model Selection and Testing Phylogeographic Diffusion in Discrete Space Phylogeographic Diffusion in Continuous Space, YFV Phylogeographic Diffusion in Continuous Space, WNV Reference Effective Sample Size Optimizing Performance Molecular Clocks Tree Priors Parameter Priors XML Reference Help FAQ Error Messages Topics Glossary What is BEAST?BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.This website is for BEAST v1.X (currently version v1.10.4). For details about BEAST2, an independent project led by the University of Auckland, please look here.What can BEAST do?Getting started with BEASTDownloading BEAST Install BEAST on Mac Install BEAST on Windows Install BEAST on UNIX/Linux or Mac command-lineIntroductory TutorialsAs an introduction to using BEAST we provide some basic introductory tutorials using the graphical applications of BEAST to perform analyses using provided example files.Citing BEAST The recommended citation for this program is: Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ & Rambaut A (2018) Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 Virus Evolution 4, vey016. DOI:10.1093/ve/vey016 BEAST is descended from earlier work:Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics, 161, 1307-1320.Rambaut A (2000) Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics, 16, 395-399.Pybus OG & Rambaut A (2002) GENIE: estimating demographic history from molecular phylogenies. Bioinformatics, 18, 1404-1405.BEAST is built on a large body of prior work and appropriate citations for individual modules, models and components will be listed when BEAST is run.BEAST-Users mailing listUsers are strongly advised to join the BEAST mailing-list. This will be used to announce new versions and advise users about bugs and problems.Send an email to [email protected] or go to the mailing list site:http://groups.google.com/group/beast-users Tags: ©2022 BEAST Developers. All rights reserved. Site uses a modified Documentation Theme for Jekyll by Tom Johnson. Site last generated: Mar 13, 2022