Module 5. Bayesian Phylogenetics

Module 5: Phylogenetics

Welcome to Module 5: Phylogenetics!

When	What
Aug 27	Day 8: Intro to Bayesian phylogenetics and BEAST, Dating trees using the fossilised birth-death process
Aug 28	Day 9: Inro to RevBayes, Morphological models and model adequacy

Software requirments

• BEAST2
• RevBayes - make sure you have v. 1.3.1 installed!
• Tracer
• FigTree
• A code editor of your choice, such as Visual Studio Code

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Day 8

Morning

• Intro in Bayesian phylogenetic inference and MCMC (Joëlle)
• The fossilized birth-death process (Laura)
• FBD model extensions (Joëlle)

Afternoon

• Brief intro to the BEAST2 pipeline (Rachel)
• Tutorial: FBD exercise in BEAST
• Open tutorial session (Rachel, Joëlle, Laura)
  • Total-evidence dating
  • BDMMPrime for Macroevolution
  • Skyline analyses for macroevolution
  • Or any other tutorial you fancy on the Taming the BEAST website

Day 9

Morning

• Bayesian inference using RevBayes (Rachel)
• Tutorial: Intro to the Rev language
• Tutorial: Tree inference using RevBayes
• FBD in RevBayes (demo only) (Joëlle)

Afternoon

• Morphological models and model adequacy (Laura)
• Tutorial: Model adequacy using RevBayes (Laura)
• Research talk (Ruolin Wu)
• Open tutorial session