MEPA11
Molecular Evolution, Phylogenetics and AdaptationCourse Timetable (provisional) |
MEPA09 | Molecular Evolution, Phylogenetics and Adaptation |
Mon, April 11th |
Day #1
|
09:30 - 11:00 |
Introduction to the course. A historical introduction to Phylogeny (Lectures) Why use phylogenies? Applications. Topology, branches, nodes and root. Rooted and Unrooted trees. Cladograms and Phylograms. |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 | Monophyletic Groups. Consensus trees. Homology and Homoplasy. Similarity. Orthology. Paralogy. Xenology. Gene trees and Species trees. Positional homology. |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 |
Molecular Evolution (Lectures) Evolutionary rates. Molecular clock. Multiple hits. Evolutionary Models. Rate heterogeneity correction. Selecting models of evolution. Modeltest. Aminoacid models. |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 |
Practical exercises: ModelTest and ProtTest using HYPHY on the Phylemon WEB SERVER. |
Tue, April 12th |
Day #2
|
09:30 - 11:00 |
Distance and Parsimony Methods. Confidence on trees. (Lectures) Ultrametric and Additive trees. Cluster Analysis. UPGMA. Neighbour Joining. Bootstrap. Newick trees. |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 |
Maximum Parsimony, Parsimony Criteria, and Tree Search. (Lectures) How many searches are there? Exhaustive Methods. Greedy algorithms. Stepwise addition. Heuristic Methods. Branch Swapping. Tree Bisection and Reconnection. |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 | Practical exercises: Phylip programs: DNAdist. Protdist. Neighbour. Seqboot. Consense. TreeView. |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 | Practical exercises: Parsimony methods. DNApars. Protpars. Phylip programs on the Phylemon WEB SERVER. |
Wed, April 13th |
Day #3
|
09:30 - 11:00 |
Practical exercises: Using MEGA for distance and parsimony method based analyses. |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 | Practical exercises: continued. |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 |
Statistical Methods I (Lectures) Maximum Likelihood. The coin example. The likelihood of a sequence. The likelihood of a one-branch tree. Real Models. Likelihood computation in a real problem. Modifying branch lengths. |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 |
Practical exercises: DNAML, PROML, PhyML. command line and Phylemon WEB SERVER |
Thu, April 14th |
Day #4
|
09:30 - 11:00 |
Statistical Methods II (Lectures) Bayesian inference. |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 | The main components of Bayes analysis. Markov Chain Monte Carlo. Prior and Posterior Probabilities. Test of Topologies. |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 |
Practical exercises: TreePuzzle. Reliability values. |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 |
Practical exercises: Testing alternative topologies. MrBayes command line and Phylemon WEB SERVER |
Fri, April 15th |
Day #5
|
09:30 - 11:00 | Evolutionary codon models. Natural selection at the molecular level (Lectures) Direct and maximum likelihood methods for sites, branches and branch-sites. |
11:00 - 11:30 | Coffee Break |
11:30 - 12:30 | Natural selection (continued) |
12:30 - 14:00 | Lunch Break |
14:00 - 16:00 |
Practical Excercises Detection of positive selection using PAML and SLR |
16:00 - 16:30 | Tea Break |
16:30 - 18:00 | Advanced final topics, Questions, and Course Overview |
Course Homepage |
Instituto Gulbenkian de Ciência, Apartado 14, 2781-901 Oeiras, Portugal Last updated: Feb 25th 2011 |