The course is broadly comprised of two parts. (i) inferring phylogenies and (ii) modeling evolutionary dynamics using phylogenies.
Exercises will involve implementing algorithms in python, and using phylogeny inference software.
Lectures and tutorials will be held online via zoom. Please use the following link to join.
https://us02web.zoom.us/j/83104595461
Please use the following doodle poll for selecting a tutorial time slot
https://doodle.com/poll/nxs74qm4mhrcisg3
An overview of the topics that will be covered is given below.
| Date | Lecture title |
|---|---|
| 3/11/2020 | Introduction and tree terminology |
| 10/11/2020 | Minimum evolution and maximum parsimony |
| 17/11/2020 | Discrete-time and continuous-time models |
| 24/11/2020 | Rate matrices and pruning algorithms |
| 1/12/2020 | Chow-Liu trees and structural EM |
| 8/12/2020 | Tree search and model optimization |
| 15/12/2020 | Mixture models for phylogenies |
| 5/1/2021 | Bayesian inference for phylogenies |
| 12/1/2021 | Divide-and-conquer approaches |
| 19/1/2021 | Identifying sites under selection |
| 26/1/2021 | Coalescent theory |
| 2/2/2021 | Molecular clocks |
| 9/2/2021 | Phylogeography |
| 16/2/2021 | Horizontal gene transfer |
| 23/2/2021 | Tumor phylogenies |