Getting Started

Data formats in bioinformatics

How to visualise phylogenetic trees and alignments

How to use PhyML

Day 1 - Phylogenetic tree reconstruction

Exercise 1 - Parameter estimation

Exercise 2 - Tree topologies

Exercise 3 - Model comparison

Exercise 4 - Branch support

Exercise 5 - Command line

Exercise 6 - Inferring ML phylogenies with codon models

Exercise 7 - Inferring ML phylogenies using real datasets

Exercise 8 - Re-Analyze published datasets

Day 2 - Detecting positive selection

Exercise 1 - Simple codon model

Exercise 2 - Branch models

Exercise 3 - Site models

Day 3.1 - Detecting episodic selection

Day 3.2 - Pipelines exercises

Solutions

Solution 1 - Parameter estimation

Solution 2 - Tree topologies

Solution 3 - Model comparison

Slides day 1

Slides

1. Markov models of substitution

2. Phylogenetic inference

3. Tree Thinking Challenge Solutions

Final challenge report