A course in the theory and practice of phylogenetic inference from DNA sequence data. Students will learn all the necessary components of state-of-the-art phylogenomic analyses and apply the knowledge to the data analyses of their own organisms.
- Instructor: Claudia Solis-Lemus, PhD
- Email: solislemus@wisc.edu
- website: https://solislemuslab.github.io/
- Class website: https://crsl4.github.io/phylogenetics-class/
By the end of the course, you will be able to
- Explain in details all the steps in the pipeline for phylogenetic inference and how different data and model choices affect the inference outcomes
- Plan and produce reproducible scripts with the analysis of your own biological data
- Justify the data and model choices in your own data analysis
- Interpret the results of the most widely used phylogenetic methods in biological terms
- Orally present the results of your own phylogenomic data analyses based on the best scientific and reproducibility practices
- Phylogenetics in the Genomic Era (open access book) by Celine Scornavacca, Frederic Delsuc and Nicolas Galtier (denoted HAL in the schedule)
- Tree thinking: an introduction to phylogenetic biology by David Baum and Stacey Smith (optional: denoted Baum in the schedule)
- The Phylogenetic Handbook by Philippe Lemey, Marco Salemi and Anne-Mieke Vandamme (optional: denoted HB in the schedule)
- The full list of papers used in this class can be found in this link