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, the course is held at the Institut Pasteur - Paris (25-28 rue du Docteur Roux 75015 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
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