Computational Biology of Infection Research
Seminar: Algorithms in phylogenetic inference and their application
The seminar "Algorithms in phylogenetic inference and their application" is hosted by the department "Computational Biology of Infection Research" at the HZI headed by Prof. Alice McHardy.
Kick-off Meeting: 11th October 2016, 4 p.m.
Room Kick-off Meeting: BRICS 046
Date: Beginning of semester break (two afternoons)
Room seminar: tba
Max. number of participants: 10
Modus: 30 minutes of presentation + 10 minutes of discussion + 3-5 pages summary
Designated for Bachelor & Master Students of Computer Science
In case you have questions about the seminar, feel free to contact Thorsten Klingen.
Description: This seminar teaches the basic principles of phylogenetic inference methods and its application. Phylogenetic trees represent the relationship between organisms, species and viruses and facilitate to reconstruct hypothetical ancestral sequences that are used to infer changes between organisms. Further, we will discuss statistical methods to test phylogenetic trees and evolutionary models. Besides phylogenetic trees, which are constructed based on substitution events in sequences; we will study phylogenetic networks, which are used to infer horizontal genetic changes e.g. recombination and reassortment events.
1) Searching the tree space
2) Parsimonious Inference
3) Distance matrix methods
4) Maximum Likelihood Inference
5) Bayesian Inference
6) Models for DNA evolution
7) Models for protein evolution
8) Measures of Selection
9) Network Inference
10) Statistics on Trees
Literature: „Inferring Phylogenies “ by Felsenstein