The course is thematically divided into two parts:
Inferring evolutionary relationships:
Methods for inferring phylogenetic trees will be introduced using the following topics
- Mechanisms of genome evolution
- Combinatorial optimization problems in phylogenetic tree inference
- Using minimum spanning trees to infer large phylogenetic trees
- Methods for rooting phylogenetic trees
- Limitations of phylogenetic trees, and alternate network-based models
Learning evolutionary dynamics using trees:
Additionally, we will cover applications of phylogenetic trees such as
- Time-calibrated trees using molecular clocks
- Identifying genomic regions under selection
- Inferring migration history
- Virus epidemiology
- Tumor heterogeneity
The course is designed for bioinformaticians, and computer scientists interested in biology.
Students will be using current software for their tutorials (Uebungen). Programming assignments are expected to be submitted as jupyter notebooks.
A familiarity with python is helpful but not necessary as it will be covered in the initial tutorials.