Advisor: Oksana Vernygora, Canadian Food Inspection Agency

Suggested co-advisors: TBD

Reconstructing evolutionary history of viruses with segmented genomes can be a very challenging and even impossible task using standard phylogenetic and phylodynamic methods which assume bifurcating branching patterns of phylogenetic trees. Shared evolutionary history of viruses that undergo reassortment has to be represented by a phylogenetic network instead of a tree. In this project we will apply new Bayesian inference framework to model evolutionary history with recombination processes. We will reconstruct reassortment networks of segmented viruses using a Markov chain Monte Carlo approach to study different aspects of the reassortment process and evolutionary dynamic of viruses with segmented genomes.

This project is suitable for one or two semesters. 

Knowledge/Skills

Basic knowledge of command line (Terminal); understanding of what phylogenetic analysis, different methods of phylogenetic inference and their underlying principles (parsimony, maximum likelihood, Bayesian inference), knowledge of R and Python; experience performing phylogenetic analysis is an asset