Graduate (Ph.D.) course the Mathematical Theory behind Phylogenetics, 5 p

19 April- 25 May 2004

Stockholm Bioinformatics Center, KI, KTH, SU
and the Ph.D. Programme in Medical Bioinformatics.


Course description

Phylogenetics is the study of evolution of, e.g., genes, genomes, organisms, etc. It has important applications in comparative genomics and comparative biology, such as orthology analysis, protein family classification, co-evolution,and organism classification. The theory behind phylogenetics includes elements from several areas in mathematics, e.g., graph theory, combinatorics and probability theory.
This course aims to provide in-depth knowledge of the mathematical basis of elementary problems in phylogenetics research. It is based on the text-book Semple and Steel, Phylogenetics, Oxford University Press, 2003 , and is given by a group of lecturers working in the field from Karolinska Institute, Royal Institute of Technology, Stockholm University, Swedish University of Agricultural Sciences and Uppsala University. A more detailed course description is available here

Location

The lectures will be held in the seminar room of Stockholm Bioinformatics Center (SBC). Directions on how to get to SBC can be found here .

Schedule

The course structure is based on the structure of the course book. Lectures will cover the main concepts of a chapter while assignments are aimed to encourage self- or group-based learning of the remainder of the chapter. Assignment are distributed at the end of the first lecture for each chapter, and there will then be an opportunity to clarify any assignments issues during the assignemnt introduction and query time.
WeekDayTimeSubject Text book chapter lecturer
17 Mon 19 Apr 10-12 Introduction - graphs Preliminaries and Ch. 1 BS
  Tue 20 Apr 10-12 X-trees and phylogenetic trees Ch. 2 BS
    13-14 Assignments: introduction and query time Preliminaries and Ch. 1-2 BS
  Thu 22 Apr 10-12 Splits 1 Ch. 3 KH
  Frid 23 Apr 10-12 Splits 2 Ch. 3 KH
    13-14 Assignments: introduction and query time Ch. 3 KH
19 Mon 3 May 10-12 Compatibility 1 Ch. 4 VM
  Tue 4 May 10-12 Compatibility 2 Ch. 4 VM
    13-14 Assignments: introduction and query time Ch. 4 VM
  Thu 6 May 10-12 Parsimony 1 Ch. 5 BS
  Fri 7 May 10-12 Parsimony 2 Ch. 5 BS
    13-14 Assignments: introduction and query time Ch. 5 BS
20 Mon 10 May 10-12 Supertrees 1 Ch. 6 AB
  Tue 11 May 10-12 Supertrees 2 Ch. 6 AB
    13-14 Assignments: introduction and query time Ch. 6 AB
21 Mon 17 May 10-12 Metrics 1 Ch. 7 LA
  Tue 18 May 10-12 Metrics 2 Ch. 7 LA
    13-14 Assignments: introduction and query time Ch. 7 LA
22 Mon 24 May 10-12 Markov models 1 Ch. 8 TB
  Tue 25 May 9.00-11.00 Markov models 2 Ch. 8 TB
    11.00-11.30 Course evaluation   BS
    11.30-12.30 Assignments: introduction and query time Ch. 8 TB

Lecturers

NOTE! Because of a foot injury, will Jens Lagergren be replaced as lecturer by Ann-Charlotte Berglund
LA Lars Arvestad, SBC, NADA, KTH
TB Tom Britton, Dept. Math Stat, SU
KH Katharina Huber, LCB, SLU
AB Ann-Charlotte Berglund, SBC, SU)
VM Vincent Moulton, LCB, UU
BS Bengt Sennblad, SBC, CGB, KI

Assesment/examination

Assessment and grading of student learning will mainly be based on the results from returned assignments given for each chapter.

Course responsible

Course responsible is Bengt Sennblad, email.

Course evaluation

The result of the course evaluation is summarized here ,

Some student-requested links

Compilation of phylogeny program at Phylip website
Workshop on phylogeny programs from 2p Introduction course in Phylogenetics theory held at SBC

Last change 5 April 2004