Computational Molecular Evolution 22115 - 2020
Week 1 (February 5): Introduction to evolutionary theory and population genetics. Models of growth, selection and mutation
- Online lectures
- Course material
- Computer exercise
Week 2 (February 12): Neutral mutations and genetic drift. Tree reconstruction by parsimony
- Online lectures
- Course material
- Computer exercise
Week 3+4 (February 19+26): Mini project 1
Building a tree from scratch: What are the closest relatives of whales?
The mini project should be submitted and assessed via the peergrade.io interface.
Week 5 (March 4): Consensus trees. Distance matrix methods
- Online lectures
- Course material
- Computer exercises
Week 6 (March 11): Models of sequence evolution. Likelihood methods
- Online lectures
- Course material
- Handout exercise: Real, Observed, and Expected Change
- Handout exercise: Computation of Likelihood
- Slides, week 6
- Lecture notes: Substitution models
- Optional lecture notes: Matrix exponentials for Markov chains
- Computer exercises
Week 7+8 (March 18 + 25): Mini project 2
Maximum likelihood and R-based phylogenetics - The origin of the Lassa and SARS-CoV-2 virus epidemics
Lassa data set: lassa.nexus
- Alignment of Lassa virus sequences encoding the transmembrane glycoprotein complex (GPC). GPC is important in the initial contact of the virus with the cells it infects and also its diffusion into the host cell. The 35 sequences include both rodent and human sequences, from a range of years, and a range of geographic locations. Names indicate location (Nig = Nigeria, Sier = Sierra Leone, Ivory = Ivory Coast, Lib = Liberia), year sampled, and host species (homo = human, nat = Mastomys natalensis, a rodent). You should use the "pinneo" strain from 1969 to root the tree (the "Pinneo" or "LP" strain of Lassa virus was isolated from the blood of Penny Pinneo, a Pioneer in Combating Lassa Fever, after a severe hemorrhagic illness acquired in Nigeria in 1969).
SARS-CoV-2 data set: See instructions in project description.
Project description: Miniproject2_corona.pdf
The mini project should be submitted and assessed via the peergrade.io interface.
Week 9 (April 1): Bayesian inference of phylogeny
- Online lectures
- Course material
- Computer exercise
Week 10 (April 15): Model Selection
- Online lectures
- Course material
- Computer exercise
Week 11 (April 22): Bayesian Phylogenetics, Part 2
- Course material
- Computer exercise
Week 12 + 13 (April 29 + May 6): Mini project 3
Bayesian and likelihood-based phylogenetics. SARS-CoV-2: selection and clock models
Project description: Miniproject3_corona.pdf
The mini project should be submitted and assessed via the peergrade.io interface.