MEPA09

Molecular Evolution, Phylogenetics and Adaptation

Course Timetable (provisional)
MEPA09 Molecular Evolution, Phylogenetics and Adaptation
Mon, March 2nd
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.
Mon, March 3rd
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.
Mon, March 4th
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
Mon, March 5th
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
Mon, March 6th
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
MEPA09 Homepage

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

GTPB Homepage

IGC Homepage

Last updated:   Jan 25th 2009