Course material will be updated throughout the semester!
| schedule | topics |
|---|---|
| Slides | tree thinking, parsimony |
| Exercise 1 | tree building using parsimony |
Homework
| schedule | topics |
|---|---|
| Slides | Intro to statistical models, graphical models, statistical consistency |
| Exercise 2 | Introduction to RevBayes and the Rev language |
Homework
Note this class will take place in the Old Library
| schedule | topics |
|---|---|
| Slides | maximum likelihood, substitution models |
| Exercise 3 | tree building using maximum likelihood |
Don’t forget next weeks exercises!!
No class
During this time we’d like you to watch the following 4 video lectures by Paul Lewis and answer a set of questions we have prepared. Paul Lewis has made numerous important contributions to the field of statistical phylogenetics, as well as producing excellent tools and materials for learning about phylogenetic theory. The videos we’ll use were developed as part of the phyloseminar series.
The videos will take about 3.5 hours to watch. Read the questions before you watch each video and write down your answers in the linked google form – we’ll go over these in week 5. Remember the goal is not to understand everything! Also make note of any questions you have after watching these and we’ll try to answer them.
| videos | topics | questions | forms |
|---|---|---|---|
| Part 1 | trees and likelihood | Questions 1 | Form 1 |
| Part 2 | trees, likelihood and rate heterogeneity | Questions 2 | Form 2 |
| Part 3a | Intro to Bayesian phylogenetics | Questions 3 | Form 3 |
| Part 3b | Intro to Bayesian phylogenetics | Questions 4 | Form 4 |
| schedule | topics |
|---|---|
| Slides | Follow up on Paul Lewis lectures |
| Exercise 4 | Bayesian tree inference |
| schedule | topics |
|---|---|
| Slides | Introduction to MCMC inference |
| Exercise 4 | Bayesian tree inference |
| schedule | topics |
|---|---|
| Slides | Bayesian timetree inference |
| Exercise 5 | Time tree inference in RevBayes |
| schedule | topics |
|---|---|
| Slides | The fossilised birth-death process |
| Exercise 6a | Exploring the FBD model assumptions |
| Exercise 6b | Dating under the FBD model in RevBayes |
| schedule | topics |
|---|---|
| Slides | Morphological evolution, model testing and model adequacy |
| Exercise 7 | Model adequacy in RevBayes |
| schedule | topics |
|---|---|
| Slides | Phylogenetic comparative methods |
| Projects page | Projects |
This course draws on material and exercises produced by Paul Lewis, Tracy Heath, Joëlle Bardio-Sottani, April Wright, Walker Pett, Joshua Justison, Sebastian Höhna, and many other RevBayesian community contributors. Thanks to Joël Koelewijn for feedback on the course content.