Lecture: Phylogeny (in English)

Classified as: Practical Computer Science, Theoretical Computer Science Lecturer: Prof. Daniel Huson Tutors: Tobias Klöpper Time: Tu, 16:15 - 18:00 h Lab: Thur, 8:00 - 10:00 h Office Hours: Daniel Huson: Thursdays 5-6pm and by appointment, C310a Tobias Klöpper: Wednesdays 9-11am. Location: A301 Requirements for admission: completed Vordiplom

Description

The first part of this course will deal with the problem of constructing phylogenetic trees from bio-molecular data. The second part of the course will deal with phylogenetic networks.

The first part of the course will be based on the following book:

Joseph Felsenstein, Inferring Phylogenies, Sinauer Associates, 2004.

Chapters: 1-8, 11-13, 16, 18.


The second part will be based on papers that will be announced during the lectures.

Content

19.10.   Overview
26.10.   Chapter 1,     Parsimony methods
 2.11.    Chapter 2,     Counting evolutionary changes
 9.11.    Chapter 3,     How many trees?
16.11    Chapter 4,     Best tree by heuristic search.
23.11.                         continued
30.11.   Chapter 5,     Finding the best tree by branch and bound
3011.    Chapter 6,     Ancestral states and branch lengths
 6.12.    Chapter 7,     Variants of parsimony
14.12.   Chapter 8,     Compatibility
21.12.                        continued
11.1.     Chapter 13,   Distance matrix methods
19.1.                           continued


The following topics are not based on Felsensteins' book:
25.1.     A.1              Quartets and splits *
1.2.       A.2              Representation of splits *
8.2.       A3              Consensus networks *
15.2.     A.4              Reticulate evolution *

*) These chapters are not part of the oral exam.

The complete script for all these lectures is available at the WSI library, Sand 14, in the scripts area.

Assignments

Assignments #1
Assignments #2
Assignments #3     Java
Assignments #4     Java
Assignments #5
Assignments #6     Java
Assignments #7
Assignments#8
Assignments#9      Java
Assignments#10
Assignments#11    Java
Assignments#12
Assignments#13    Data

Script (written by students)

02_11.pdf
09_11.pdf
30_11.pdf
16_11a.pdf
16_11.pdf
07_12.pdf
14_12.pdf
18_01.pdf
01_02.pdf

Requirements

For students in their 5. semester or higher., with "Vordiplom".

Credits for problem sessions

To obtain credits for attending the problem sessions, you are required to regularly and actively participate in the problem sessions. Additionally, you must regularly hand in assignment sheets and obtain at least 60 % of all possible assignment points. Students are permitted to work in groups of up to two people per hand-in.