“Large phylogenies” is a half-day module withing the “Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology” (VEME) workshop.
This module aims discusses approaches to reconstruct large trees and to perform downstream cluster analyses on such trees. In includes 4 sessions:
- Fast methods for large phylogenies (theory) – Heiko Schmidt
This part introduces different approaches implemented in software to facilitate the
reconstruction of large trees with many taxa. The lecture will cover aspects like fast
methods and parallel computing. It also discusses problems and pitfalls of running such
- Partition of large phylogenetic trees (theory) – Anna Zhukova
The lecture will introduce ancestral character reconstruction and its applications to study
the evolution of characters along phylogenetic trees, with emphasis on phylogeography and
detection of geographic clusters of virus spreads.
- Inferring large trees: practice – Heiko Schmidt
Here we will demonstrate and discuss different software and command line options that can
be useful to reconstruct large trees.
- Cluster analysis: practice – Anna Zhukova
In the practical session we demonstrate the use of PastML to reconstruct the geographic
spread of a virus by performing an ancestral character reconstruction for sampling locations.
We will compare different methods and assess the uncertainty of predictions in different
parts of the tree.