053522 VU Bioinformatics for phylogeny and evolutionary tree reconstruction (2023W)

Overview: Phylogenetics is the research field that deals with the reconstructions of evolutionary relationships of biomolecules like DNA and proteins, organisms or viruses. It is, thus, fundamental to many biological analysis such as epidemiology surveillance.
a. Aims: Understanding of the bioinformatics concepts and methods of phylogenetics and evolutionary tree reconstruction in theory and practice;
b. Content: The course aims at giving a broad overview covering topics like historical background; theoretical basics and definitions; different approaches like maximum parsimony, distance methods, maximum likelihood and Bayesian and associated algorithms; tree search and tree rearrangements; models of sequence evolution and model selection; summarizing trees and branch support; tree topology testing; tracing phylogenetic signal and noise; phylogenomics, supertrees and partition models; ancestral state reconstruction, phylogeography.
c. Methods: Lectures, graded exercises (submitted via Moodle), finally, the course includes two practical units applying phylogenetic software.