GTPB

The Gulbenkian Training Programme in Bioinformatics


GTPB runs at the Instituto Gulbenkian de Ciência on a yearly basis since 1999.
More than 950 course attendees in 9 years
Pedro Fernandes, GTPB organizer


Molecular Evolution, Phylogenetics and

Adaptation

MEPA08 course website

IMPORTANT DATES
Deadline 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.

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.

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.

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Instituto Gulbenkian de Ciência, Apartado14, 2781-901 Oeiras, Portugal


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Last updated:Apr 2nd 2008