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Introduction to Molecular Phylogeny

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M2-E34 IntroductionTo MolecularPhylogeny Planning2020

Master in Life Science, ENS
Bio-M2_E34 | Introduction to Molecular Phylogeny
Year : 2 (M2)
Semester : 1 (S1)
Duration : 25h / 5 days, from 14th to 18th December, 2020


Catherine Dauga, Institut Pasteur
Contact ENS : Denis Thieffry


9h30-17h30 | 50/50 theoretical classes and computer-training sessions every day. Includes three courses / conferences for a wider audience.




Molecular phylogenetics, distance, parsimony, maximum likelihood

Course prerequisites

Familiarity with sequence databases,
Basic bioinformatics software (BLAST, multiple alignment...),
Basic concepts in probability (independent events, conditional probability, usual distributions),
Basic concepts in statistics (tests, correlation, regression, parameter estimation),
Computer handling.

Course objectives and description

Introduction to Molecular Phylogenetics : Concepts, Methods and Interpretation
Aims : 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 analyse their own data, to interpret the resulting phylogenies, and to measure the limits and potential drawbacks of phylogenetic approaches.
Themes : This course offers training in molecular phylogenetics with theoretical presentations on the four main approaches to infer phylogenetic trees : distance, parsimony, maximum likelihood and Bayesian. We explain the general concepts behind these methods, how to master the choices and options, and interpret the results of phylogeny programs. We also present the methods used for building trees from genome data, dating past events, and inferring ancestral sequences and character states, as well as applications of these methods in molecular epidemiology. This course gives a large room to exercises and hands-one sessions on standard phylogeny programs.


Students will be assessed daily based on multiple-choice questions.

Course material

Slides from the presentations.

Suggested readings in relation with the module content

• AD Young and JP Gillung (2020). Phylogenomics – principles, opportunities and pitfalls of big-data phylogenetics. Systematic Entomology 45 : 225-47.
• L Philippot, SG Andersson, TJ Prosser, JP Schimel, WB Whitman and S Halli (2010). The ecological coherence of high bacterial taxonomic ranks. Nature Reviews Microbiology 8 : 523-9.
• A Rieux and F Balloux (2016). Inferences from tip-calibrated phylogenies : a review and a practical guide. Molecular Ecology 25 : 1911-24.
• T Warnow (2018). Computational Phylogenetics : An Introduction to Designing Methods for phylogeny estimation - Chapter 8 statistical gene tree estimation methods. Cambridge University Press.
• O Gascuel (2005). Mathematics of Evolution and Phylogeny. Oxford University Press.