Phone: (+49 30) 8413 1150 - Fax: (+49 30) 8413 1394
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Max Planck Institute for Molecular Genetics - IhnestraÃe 63-73 - 14195 Berlin - Germany - Phone: (+49 30) 8413 1150 - Fax: (+49 30) 8413 1394 |
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The course will cover the algorithmic and statistical methods used for the construction of phylogenetic trees from biomolecular sequences, in particular:
It comprises a lecture with tutorials (A), focussing on the algorithms and supporting theory and a seminar series (B), which is devoted to it's application. It is recommended to select both A and B but not required. Student with a solid background in phylogeny from the Algorithmic Bioinformatics lecture should be able to follow the seminars. Examinations for the course will be held on March 16th and 17th in the office of Prof. Martin Vingron at the MPI for Molecular Genetics.
| Event | Date | Time | Location | Notes |
|---|---|---|---|---|
| Lectures (A) | Wednesdays | 16:00 – 18:00 | Takustr. 9, SR005 | |
| Exercises (A) | Mondays | 16:00 – 18:00 | Takustr. 9, SR051 | Alternating with seminars |
| Seminar (B) | Mondays | 16:00 – 18:00 | Takustr. 9, SR051 | Nov, 16th and 30, Dec 14th and Jan, 11th |
| Date | Type | Topic | Lecturer |
|---|---|---|---|
| Oct 19, 2009 | Seminar | Introduction | Krause, Vingron |
| Oct 21, 2009 | Lecture | Overview molecular evolution | Krause |
| Oct 26, 2009 | Tutorial | Exercise 0 | |
| Oct 28, 2009 | Lecture | Substitution models for sequences | Vingron |
| Nov 2, 2009 | - | Keine Veranstaltung (no event) | |
| Nov 4, 2009 | Lecture | Distance based phylogenies | Vingron |
| Nov 9, 2009 | Tutorial | Exercise 1 | |
| Nov 11, 2009 | Lecture | Parsimony methods | Krause |
| Nov 16, 2009 | Seminar | BioNJ The prokaryotic tree of life | Simon Schäfer Konrad Rudoplh |
| Nov 18, 2009 | Lecture | Markov chains and Maximum Likelihood | Vingron |
| Nov 23, 2009 | Tutorial | Exercise 2 | Krause |
| Nov 25, 2009 | (Lecture) | No event - Entfällt | |
| Nov 30, 2009 | Seminar | The entrails of chicken (verschoben) | Nikolas Balcazar |
| Dec 2, 2009 | Lecture | Ausgefallen wegen Generalversammlung | Krause |
| Dec 7, 2009 | Tutorial Seminar | Exercise 3 Distance metrices on trees | Kendell Clement |
| Dec 9, 2009 | Lecture | Gene duplications - orthology and paralogy | Krause |
| Dec 14, 2009 | Seminar | Coelomata vs. Ecdysozoa | Jevgeni Erehman |
| Dec 16, 2009 | Lecture | Quartet-based methods for phylogenies | Vingron |
| Jan 4, 2010 | Tutorial | Exercise 4 | |
| Jan 6, 2010 | Lecture | Bayesian methods and Monte Carlo Markov chains | Vingron |
| Jan 11, 2010 | Seminar | Evolution of interaction networks Co-estimation of alignment and trees | Konstantin Pentcher Birte Kehr |
| Jan 13, 2010 | Lecture | Reticulate trees and phylogenetic networks | Krause |
| Jan 18, 2010 | Tutorial | Exercise 5 | |
| Jan 20, 2010 | Lecture | Consistency and invariants | Vingron |
| Jan 25, 2010 | Seminar | EM for phylogenetic inference | Matthias Lienhard |
| Jan 27, 2010 | Lecture | Neutral evolution and selection | Vingron |
| Feb 1, 2010 | Tutorial | Exercise 6 | |
| Feb 3, 2010 | Lecture | PhyloHMMs | Vingron |
| Feb 10, 2010 | Lecture | Coalescence | Vingron |
| Feb 14, 2010 | Tutorial | Exercise 7 | |
| Feb 17, 2010 | Lecture | Genome Evolution | Peter Arndt |
| Feb 22, 2010 | Tutorial | Review | Krause |
| Feb 24, 2010 | Lecture | Genome Evolution | Peter Arndt |
| March 16, 2010 | Examination (9:00 -/ 10:00 ) | Vingron/Krause | |
| March 17, 2010 | Examination (9:00 / 10:00) | Vingron/Krause |