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 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

BEAST Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7: versions since June 2003  Increasing range of models implemented >150 publications Java platform Open source

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

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

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

Running BEAST

Tracer: Analyzing BEAST output

Phylogenetic Analysis

Demographic history

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?

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