Lecture: Phylogenetic Networks

 

Lecturers	Prof. Dr. Daniel Huson and Dr. Regula Rupp
Lectures	Wednesday 8:30-10:00, Kleiner Hoersaal, Sand 6/7
Problem sessions	1 hour per week, time and place to be announced
Target audience	Diploma- and master-students
Modules	See "Modulhandbuch"
Language	English

Contents

The topic of this course is phylogenetic networks. The course is based on a draft of the book "Phylogenetic Networks" which is currently being written by Daniel Huson and Regula Rupp. The book will be published next year by Cambridge University Press.

The first three lectures will cover the topic of phylogenetic trees and will focus on the problem of reconstructing phylogenetic
trees using sequence-based methods, such as maximum parsimony, maximum likelihood and Bayesian inference, and
using distance-based methods.

The second three lectures will focus on rooted phylogenetic networks, introducing the concept of a cluster network, 
discussing how to compute unrooted phylogenetic networks, looking at different topological restrictions on them (such as galled trees, galled networks and level-k networks) and will also deal with problems such as the cluster containment problem.

After the midterm exam, the course will focus on unrooted phylogenetic networks, in particular split networks. We will discuss how
to compute such networks and how to draw them.

The last three lectures will look at different algorithms that compute phylogenetic networks from trees, distances and sequences.

Schedule

15.10.2008	Basics
22.10.2008	Phylogenetic Trees I
29.10.2008	Phylogenetic Trees II
5.11.2008	Rooted Phylogenetic Networks I r
12.11.2008	Rooted Phylogenetic Networks II h
19.11.2008	Rooted Phylogenetic Networks III
26.11.2008	Rooted Phylogenetic Networks IV
3.12.2008	Midterm Examination
10.12.2008	Unrooted Phylogenetic Networks I
17.12.2008	Unrooted Phylogenetic Networks II
7.1.2009	Unrooted Phylogenetic Networks III r
14.1.2009	Unrooted Phylogenetic Networks IV
21.1.2009	Phylogenetic Networks from Distances r
28.1.2009	Phylogenetic Networks from Sequences r
4.2.2009	Final Examination

Credits for this course:

Master students:
This course is worth 4 LP, so you will be expected to do 4x30=120 hours of work for this course. You have to take part in the problem sessions and have to hand in solutions to the exercise sheets. For this, you can work in groups of up to two people. You will be graded on the number of points that you obtain and also on your participation in the problem sessions. This grade will make up 1/3 of your final grade. The mid-term exam and final exams will each also contribute 1/3 toward your final grade.

 

Diploma students:
To get credit for this course, you must obtain a grade of 4 or better as described under Master students.
Diese Veranstaltung ist prüfbar als Praktische Informatik (2+2 SWS) or Theoretische Informatik (maximal 2+2 SWS). 

Exercises:

• Exercises 1
• Exercises 2
• Exercises 3          script
• Exercises 4
• Exercises 5: these exercises will take place in the tutorial on Monday, Nov 24th.
• Exercises 6
  
• Exercises 7
• Exercises 8
• Exercises 9
• Exercises 10
• Exercises 11
• Exercises 12