ACGT Tutorials

Getting Started

    Data formats in bioinformatics How to visualise phylogenetic trees and alignments How to use PhyML

Day 1 - Phylogenetic tree reconstruction

    Slides day 1 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

    Slides day 2 Exercise 1 - Simple codon model Exercise 2 - Branch models Exercise 3 - Site models

Day 3.1 - Detecting episodic selection

    Exercise 7

Day 3.2 - Pipelines exercises

    Pipelines

Solutions

    Solution 1 - Parameter estimation Solution 2 - Tree topologies Solution 3 - Model comparison

Slides day 2

Slides

1. Detecting Positive Selection


References
  1. Detecting and understanding natural selection, Maria Anisimova and David A. Liberles

  2. Selection on the Protein-Coding Genome, Carolin Kosiol and Maria Anisimova


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