Advances in sequencing technology have made it possible to investigate the evolutionary dynamics of rapidly evolving pathogens such as SARS-CoV2 in unprecedented detail. Phylogeny inference is an essential step in evolutionary analysis. Thus techniques for large-scale phylogeny inference are needed if one is to study the evolution of tens of thousands of viral genomes. Students participating in this seminar will be introduced to topics such as
(i) Tree modification operations
(ii) Numerical optimization of hidden Markov models on trees
(ii) Topological correspondence between minimum spanning trees and phylogenetic trees
(iii) Evolutionary placement algorithm
Participation in the course "Phylogeny inference and applications", or any course dealing with combinatorial optimization is helpful but not necessary.