BIOINF3310 Phylogeny and Evolution
| Lecturer | Prof. Daniel Huson |
| Lectures | Thursdays, 16:15-18h, C215, Sand 14 |
| Assignments | Assignments will be made available every Thursday at 16:00h via Ilias. Solutions are due on the following Thursday at 16:00h. |
| Tutorials | Tutorials: Tuesdays, 16:15-18h, A302, Sand 13, start on 3.11. Participation is mandatory. |
| Exam | Written exam, weekly quizzes |
| Audience | Bachelor (and master) students: bioinformatics and medical informatics, 6 LP |
| Language | English |
| Links | Alma Ilias |
Contents
This course gives an introduction to the basic concepts and methods of phylogenetics, with an emphasis on phylogenetic networks. Here is a tentative schedule:
| Date | Topic | Assignments |
|---|---|---|
| 20.10. (Tuesday, A302, Sand 13) | 1. Graphs and trees | Assignment 1+2 |
| 22.10. | 2. Counting trees and tree neighborhoods | |
| 29.10. | 3. Maximum parsimony (Some overlap with Sequence Bioinformatics) | Assignment 3 |
| 5.11. | 4. A simple model of evolution (Some overlap with Sequence Bioinformatics) | Assignment 4 |
| 12.11. | 5. Distance-based method (Some overlap with Sequence Bioinformatics) | Assignment 5 |
| 19.11. | 6. Rooted trees and networks | Assignment 6 |
| 26.11. | continued | Assignment 7 |
| 03.12. | 7. Unrooted trees and networks | Assignment 8 |
| 10.12. | continued | Assignment 9 |
| 17.12. | 8. Consensus trees and networks | Assignment 10 |
| 7.01. | 9. Neighbor net | Assignment 11 |
| 14.01. | 10. Phylogenetic outlines | Assignment 12 |
| 21.01. | 11. Phylogenetic diversity | Practice exam |
| 28.01. | 12. Trees vs. networks | |
| 02.02. (Tuesday) | EXAM, TBA | |
| Makeup exam | 31.3.2026 10-12h in TBA |
There will be a makeup exam on 31.3.2026. Please send an email to Prof. Daniel Huson if you intend to participate in this exam.
Recommended textbooks
- Selected chapters of: Huson, Sequence Bioinformatics, Draft
- Stadler et al, Decoding Genomes: From Sequences to Phylodynamics, decodinggenomes.org, 2024.
- Huson, Rupp und Scornavacca, Phylogenetic Networks, Cambridge University Press, 2010
- Felsenstein, Inferring Phylogenies, Sinauer, 2004
How to get credit for this course
- Always participate in the weekly problem sessions and actively present your results. If you miss more than two tutorials, then you will not be allowed to take the exam.
- Assignments are set weekly and are due the following week, you need to complete 50% to qualify for the exam.
- There will be weekly quizzes in the tutorials on the assignments, you must pass 50% to qualify for the exam.
- Pass the exam.