BIOINF3310 Phylogeny and Evolution
| Lecturer | Prof. Daniel Huson |
| Lectures | Tuesdays, 16:15-18:00, in C118a Sand 14 |
| Assignments | Assignments will be made available every Tuesday at 16:00h via Ilias. Solutions are due by the following Tuesday at 16:00h. |
| Tutorials | Tutorials: Thursdays , 16:15-18h C215, Sand 14, starting 31st. October 2024. Participation is mandatory. |
| Exam | Written exam |
| Audience | Bachelor students, bioinformatics and medical informatics, 6 LP Master students, bioinformatics |
| 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 |
|---|---|---|
| 17.10. | 1. Graphs and trees | Assignment 1 |
| 22.10. | 2. Counting trees and tree neighborhoods | Assignment 2 |
29.10..
| 3. Maximum parsimony (Video only, no class) (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. Maximum-Likelihood (Some overlap with Sequence Bioinformatics) | Assignment 5 |
| 19.11.. | 6. Distance-based method (Video only, no class) (Some overlap with Sequence Bioinformatics) | Assignment 6 |
| 26.11. | 7. Rooted trees and networks | Assignment 7 |
| 03.12. | continued | Assignment 8 |
| 10.12. | 8. Unrooted trees and networks | Assignment 9 |
| 17.12. | continued | Assignment 10 |
| 07.01. | 9. Consensus trees and networks | Assignment 11 |
| 14.01. | 10. Neighbor net | Assignment 12 |
| 21.01. | 11. Phylogenetic outlines | Practice exam |
| 28.01. | continued | |
| 06.02. | EXAM, location TBA |
There will be a makeup exam on April 3rd, 10-12h, F119, Sand 6/7 . Please send an email to Prof. Daniel Huson if you intend to participate in this exam.
Recommended textbooks
- 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.
- Obtain at least 50% of all points. If you obtain 70%, 80% or 90% of all possible assignment points, then you will receive bonus points toward your exam.
- Pass the exam.