Bayesian Evolutionary Analysis by Sampling Trees (BEAST)

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Bayesian Evolutionary Analysis by Sampling
Trees(BEAST)
LEE KIM-SUNG Environmental Health
Institute National Environment Agency
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Analysis of Sequence Variation

• Polymorphisms
• Phylogenetics
• Statistic and evolution
• Parameter estimation
• Hypothesis testing

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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

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BEAST

• Drummond AJ, Rambaut A (2007) "BEAST Bayesian
  evolutionary analysis by sampling trees." BMC
  Evolutionary Biology 7214
• 23 versions since June 2003
• Increasing range of models implemented
• gt150 publications
• Java platform
• Open source

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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

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

• A graphical user interface for generating BEAST
  XML input files for a number of model
  combinations

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Running BEAST
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Tracer Analyzing BEAST output
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Phylogenetic Analysis
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Demographic history
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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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Thank You