The Gulbenkian Training Programme in Bioinformatics
Molecular Evolution, Phylogenetics and Adaptation MEPA08 course websiteIMPORTANT DATESDeadline for applications: March 25th 2008 Course date: April 14th - April 18th 2008 |
Instructors: |
Hernan Dopazo is the head of the Comparative Genomics Unit at the CIPF (Valencia) and leads the PHYLEMON project (http://phylemon.bioinfo.cipf.es ). He obtained his Ph.D. Degree in the National History Museum of Madrid and has held postdoctoral positions in the National Center for Oncologic Research (Madrid), the Institute for Biomedical Research (Argentina), the CEA-UBA's Complex Systems Research Group (Argentina), and at the FCEN's Vertebrate Paleontolgy Laboratory (Argentina). He has taught Evolutionary Theory and Phylogenetics for more than ten years at the UBA (Argentina), the UAM (Madrid), CIPF (Valencia), University of Cambridge (UK), Instituto Gulbenkian de Ciência (Portugal), and others. His main interests are within the fields of phylogenomics, comparative genomics, and natural selection and its relation to disease.
Bioinformatics Department, CIPF, Valencia.
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Leonardo Arbiza obtained his Degree in Biochemistry and
Molecular Biology (Boston Universty) and a Master's Degree in Biochemistry
and Biotechnology (UFV, Spain). Currently he is part of the Comparative
Genomics Unit in the Department of Bioinformatics at the CIPF (Valencia)
where he is involved in the PHYLEMON (http://phylemon.bioinfo.cipf.es )
project. His main research interests fall within the fields of comparative
genomics and evolution with particular interest in the detection of natural
selection and the understanding of forces driving organism specific variation.
He has taught training courses like this one at CIPF (Valencia),
University of Cambridge (UK), Instituto Gulbenkian de Ciência (Portugal),
and others.
Bioinformatics Department, CIPF, Valencia.
|
Course description:
More than 30 years ago, Theodosius Dobzhansky claimed:"Nothing in Biology makes
sense except in the light of evolution": Currently, the simplest Bioinformatics
analysis uses species comparisons in order to hypothesise the function of an
novel biological sequence: Moreover, in most Molecular Biology labs,
evolutionary and phylogenetic concepts are constantly being used with more or
less formality: homology, similarity, evolutionary rates, long branch
attraction, rooted and unrooted trees, monophyletic group, molecular clock,
adaptation, lineage effects, neutralism, cladograms, phylograms, etc: The course
covers these and other major concepts in Evolutionary Biology and Phylogenetics:
Attendees will acquire specific skills in using the methodology in Comparative
and Evolutionary Biology problems: The course is designed to be a mixture of
theoretical and practical sessions developed in 5 days, where both classic and
recently introduced methods for phylogenetic reconstruction will be covered: As
outcome of the more recent developments, the course dedicates a day to the
analysis of adaptation at a molecular level: Phyml, Phylip, MEGA, TreePuzzle,
MrBayes, PAML, Modeltest-Protest, and the Phylemon web server are some of the
software resources that will be used in the practical sessions: Elementary
knowledge of Biochemistry and Sequence Analysis is useful though not strictly
required.
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Course Timetable |
April 14th |
Day 1 |
09:30 -11:00 |
A historical introduction on Phylogeny (Lectures) Why use phylogenies? Applications. Topology, branches, nodes & root. Rooted & Unrooted trees. Cladograms & Phylograms. |
11:00 -11:30 |
Coffee Break |
11:30 -12:30 |
Monophyletic Groups. Consensus trees. Homology and Homoplasy. Similarity. Orthology. Paralogy. Xenology. Gene trees & 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. |
April 15th |
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. |
April 16th |
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 - 15:30 |
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 & Phylemon WEB SERVER |
April 17th |
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 & Phylemon WEB SERVER |
April 18th |
Day 5 |
09:30 - 10:30 |
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 - 15:30 |
Practical Excercises Detection of positive selection using PAML and SLR |
15:30 - 16:00 |
Tea Break |
16:00 - 17:30 |
Advanced final topics, Questions, & Course Overview |
Pre-requisites:
Basic Molecular Biology and Biochemistry. Elementary computing skills. |
Instituto Gulbenkian de Ciência,
Apartado14, 2781-901 Oeiras, Portugal