Module 7: Phylogenetics

When What
Sept 5 Day 12: Intro to tree building, substitution models and Bayesian inference
Sept 6 Day 13: Phylogenetic dating using the fossilised birth-death process
Sept 7 Day 14: Model selection, model adequacy, beyond topology

Required software

Please download and install the following software before the class on Monday.

Day 1

When What
AM Introduction to tree building
AM Exercise 1: Snack phylogeny
AM Exercise 2: Parsimony demo
AM Introduction to model based phylogenetics
AM Exercise 3: Likelihood
PM Brief intro to Bayesian inference and MCMC
PM Introduction to RevBayes and Rev langauge
PM Exercise 4: the Rev language
PM Exercise 5: Bayesian tree inference using RevBayes

Day 2

When What
AM Recap: the Rev langauge
AM Recap: Exercise 5
AM Introduction to divergence dating
AM Exercise 6: divergence dating
PM Exercise 7: Snack phylogeny
PM The fossilised birth-death process
PM Exercise 8: Simulating trees and fossils
PM Exercise 9: dating under the FBD process

Day 3

When What
AM Recap: Exercise 9
AM Morphological models
AM Exercise 10: morphological models in RevBayes
PM Bayesian model selection
PM Exercise 11: Model selection
AM Model adequecy
PM Exercise 12: Model adequecy using RevBayes
PM Beyond topology: PCMs



via GIPHY

Acknowledgements

This course draws on material and exercises produced by Josh Drew, Paul Lewis, Tracy Heath, Joëlle Bardio-Sottani, April Wright, Walker Pett, Joshua Justison, Sebastian Höhna, and many other RevBayesian community contributors.