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Bayesian Evolutionary Analysis by Sampling Trees (BEAST)

Bayesian Evolutionary Analysis by Sampling Trees (BEAST). LEE KIM-SUNG Environmental Health Institute National Environment Agency. Analysis of Sequence Variation. Polymorphisms Phylogenetics Statistic and evolution Parameter estimation Hypothesis testing. BEAST.

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Bayesian Evolutionary Analysis by Sampling Trees (BEAST)

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  1. Bayesian Evolutionary Analysis by Sampling Trees(BEAST) LEE KIM-SUNG Environmental Health Institute National Environment Agency

  2. Analysis of Sequence Variation • Polymorphisms • Phylogenetics • Statistic and evolution • Parameter estimation • Hypothesis testing

  3. BEAST • Framework for parameter estimation and hypothesis testing of evolutionary models • Bayesian statistical framework • Combination of prior knowledge and data information • Cross-platform for Bayesian MCMC analysis of molecular sequences

  4. BEAST • Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology7:214 • 23 versions since June 2003 • Increasing range of models implemented • >150 publications • Java platform • Open source

  5. What can BEAST do? • Molecular clock models • constant, variable (relaxed) • Non-contemporaneous sequences (tipdate) • Local clock • Coalescent models • Population size and growth • Multi-locus • Estimation of divergence date • Substitution model heterogeneity across sites • Flexible model specification

  6. BEAST Workflow Sequence alignment Specify parameters and models Generating XML in Beauti Running BEAST Tracer Analyzing BEAST output Low ESS Tree Annotater

  7. Beauti : Generating XML file • A graphical user interface for generating BEAST XML input files for a number of model combinations

  8. Running BEAST

  9. Tracer: Analyzing BEAST output

  10. Phylogenetic Analysis

  11. Demographic history

  12. Grid Enabled BEAST? • BEAST performance • dictated by speed of likelihood evaluation at each state •  dataset,  parameter   running time • e.g. Phylogeographic analysis •  11 days (Core 2 Duo, 2.8 GHz, 4GB RAM) • 5 days (Mac Cluster) • Possibility of Grid computing for BEAST?

  13. Thank You

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