Algorithmen der Bioinformatik

BIOINF3310  Phylogeny and Evolution

LecturerProf. Daniel Huson
LecturesTuesdays, 16:15-18:00, in C118a Sand 14
AssignmentsAssignments 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.

ExamWritten exam
Audience

Bachelor students, bioinformatics and medical informatics, 6 LP

Master students, bioinformatics

LanguageEnglish
LinksAlma 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:

DateTopicAssignments
17.10.1. Graphs and treesAssignment 1
22.10.2. Counting trees and tree neighborhoodsAssignment 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 networksAssignment 7
03.12.continuedAssignment 8
10.12.8. Unrooted trees and networksAssignment 9
17.12.continuedAssignment 10
07.01.9. Consensus trees and networksAssignment 11
14.01.10. Neighbor netAssignment 12
21.01.11. Phylogenetic outlinesPractice 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.