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

How to visualise phylogenetic trees and alignments

Visualising Multi-Sequence-Alignments using Aliview

Discovering nucleotide/amino-acid variations in a MSA can be tricky. One way to help the user to overcome this issue is using dedicated softwares that allow basic operations on the MSA object (i.e. alignment browsing, coloring, indexing and nucleotide/amino-acid translation).

1. Open a MSA file

2. Perform a view

3. Extract view

4. Summary statistics on the view

5. Translate a selection view using different codon frames

Other visualization softwares

You can find a list of MSA visualizers here: https://en.wikipedia.org/wiki/List_of_alignment_visualization_software

Visualizing phylogenetic trees with FigTree