Instructor(s): Julia A. Palacios and Nicola F. Müller
General
This module covers the use of phylogenetic and bioinformatic tools to analyze pathogen genetic variation and to gain insight into the processes that shape their diversity. The module focuses on phylogenies and how these relate to population genetic processes in infectious diseases.
In particular, the module will cover Bayesian Evolutionary Analysis by Sampling Trees 2 (BEAST2). Class exercises will focus on estimating epidemic time scales, reconstructing changes in viral population sizes through time, and inferring spatial diffusion of viruses. Evolutionary processes including recombination and selection will also be considered.
Before the course
Please install the newest version (2.7.7) of BEAST2 on the computer you plan to use. BEAST2 requires Java. If you encounter installation issues, post in the SISMID Slack channel module-evolution-and-molecular-epi-of-viruses.
Also install:
- Tracer 1.7.2 to visualize MCMC traces.
- Figtree 1.4.4 to view phylogenies. If you get a Java error, try Figtree 1.4.5_pre.
Schedule
| Time | Monday, July 14 | Tuesday, July 15 | Wednesday, July 16 |
|---|---|---|---|
| 9:00 am |
Introduction to Bayesian Phylogenetics and BEAST
Julia |
||
| 11:00 am |
Structured Birth–Death Models
Nicola |
alternative approaches
Julia & Nicola |
|
| 11:30 am |
Q&A and wrap-up
Julia & Nicola |
||
| 1:00 pm |
Understanding BEAST output and results
Nicola |
||
| 1:30 pm |
Tree Distances, Summaries, and Convergence
Julia |
||
| 2:00 pm |
Visualizing and Interpreting Trees
Julia |
||
| 3:30 pm |
Recombination and Reassortment
Nicola |
Some Reading Material (optional)
- Overview of BEAST2 packages: doi:10.1371/journal.pcbi.1006650
- Decoding Genomes: decodinggenomes.org
- Review of phylodynamics (coalescent focus): PLoS Comput Biol 100.2947
- Review of phylodynamics in livestock: ScienceDirect S0169534721001300
Acknowledgements
These tutorials are, in part, from taming-the-beast.org and past SISMID workshops, based on work by Louis du Plessis, Veronika Boskova, David Rasmussen, Carsten Magnus, Sebastian Duchene, Timothy G. Vaughan, Denise Kühnert, Julia Pecerska, Marc Suchard, and Philippe Lemey.