This repository contains a tutorial for molecular phylogenetics prepared for a teaching demonstration. The exercise demonstrates how to build the hypothesis for a phylogenetic tree of primates based on a single gene. It is designed as a jupyter notebook using Python and the BioPython library.
The notebook with some small exercises can be found in phylogenetics-tutorial-exercise.ipynb.
phylogenetics-tutorial-solution.ipynb contains the example solutions. The folders data and scripts contain the data used
in the exercise and the scripts to prepare the data, respectively.
The accompanying slides for the teaching demonstration can be found here.
You can find more information on the topics covered in this tutorial and advanced methods here:
- Introduction to phylogenetics: a good and accessible overview.
- UPGMA: A more in-depth tutorial.
- Evolutionary correction: A tutorial that includes the discussion of corrections to model multiple substitutions at a given site.
- Neighbor Joining: Neighbor Joining approaches for building phylogenetic trees that remove the assumption of a constant mutation rate.
- Bayesian approaches: Bayesian approaches for building the trees that provide likelihood estimates.
Textbooks on the topic:
- Joseph Felsenstein: Inferring Phylogenies
- Lemey, Salemi & Vandamme: The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing