Introduction to Molecular Phylogeny

The purpose of the course of molecular phylogeny is to bring theoretical knowledge and good practices for data analysis using specialized softwares. This course is open to doctoral trainings and professionals of the INCEPTION program.

This course aims to provide an in-depth understanding of the methods used in phylogenetics, and good practices of the main programs used in the field. It will allow students to analyze their own data, to interpret the resulting phylogenies, and to measure the limits and potential drawbacks of phylogenetic approaches.

The course is organized over one week, with 50/50 theoretical classes and computer-training sessions every day. Three course/conferences are given for a wider audience.

This year, all classes are held at the Institute of Biology of the Ecole Normale Supérieure (IBENS, 46 rue d’Ulm, 75005 – Paris).

Overall Program of the course

Theoretical courses on phylogeny’s concepts (15 h) alternating with practical courses using computer based tools and phylogeny softwares (15h)

Introduction to phylogeny : General principles of tree inference and applications to infectious disease monitoring

Tree handling, rooting, reading and interpretation

Mathematics (simple) of trees and evolutionary models

Distance methods and reliability (bootstrap, consensus …)

Parsimony Methods, algorithms, long branch attraction (LBA)

Maximum likelihood Methods, quick branch tests

Bayesian Approach: Bayes theorem, MCMC, and posterior probabilities

Evolutionary processes and detection of positive selection

Choice of methods, artefacts and phylogenetic conflicts

Phylogenomics

Registration

This course of ongoing fromation is open to professionals from the Institut Pasteur in Paris or on the International Network of Institut Pasteur. Supported by the INCEPTION program, the course is open to doctoral training of all INCEPTION partners.

To register, please contact : Inception-phylogeny-training@pasteur.fr

For people working at Institut Pasteur, registration has to be done with : drh-formation

Essential prerequisites:

Be familiar with sequence databases

Have already used basic software in bioinformatics (BLAST, multiple alignment .....)

Know basics in probability and statistics (tests, usual distributions, simple estimation methods of parameters)

Applications will be accepted within the limit of 18 places available.

Supported by the Inception program, the continuing education and the Computational Biology Department of the Institut Pasteur, this course is free.