GENE0448-2 : Phylogenetic methods

Study Programmes 2015-2016

GENE0448-2

Phylogenetic methods

Duration :

20h Th, 30h Mon. WS

Number of credits :

Master in bio-informatics and modelling (120 ECTS)		5

Lecturer :

Denis Baurain

Language(s) of instruction :

French language

Organisation and examination :

Teaching in the first semester, review in January

Units courses prerequisite and corequisite :

Prerequisite or corequisite units are presented within each program

Course contents :

This course aims to provide the theoretical and practical bases of phylogenetic methodology.

Reminder on (molecular) phylogenetics
Sequence alignment - global alignment (NW), local alignment (SW, BLAST), multiple alignment (ClustalW) and profiles
Parsimony - phylogenetic trees, tree length (Fitch's algorithm) and search heuristics
Distance methods - distance matrices, W(U)PGMA, NJ and models of sequence evolution
Probabilistic methods - likelihood (principle, algorithms, models, advantages and model selection), statistical support and congruence, Bayesian inference (principle and algorithms), relaxed molecular clocks
Phylogenomics - principle, stochastic and systematic errors, supertrees, supermatrices, CAT model, applications

Learning outcomes of the course :

Theory: At the end of this course, students will be able to explain the main concepts, methods and algorithms used in phylogenetics. They will have an intuitive understanding of probabilistic methods and will be able to justify their preferential use over other approaches. This requires, above all, to have UNDERSTOOD the course material. In this sense, this course is probably different from some other subjects of the curriculum in biology, in which mere memorization may be enough to pass the examination.
Exercises: For some algorithms (specified in class), an APPLICATION using pen and paper to solve a toy example may be requested.
Applications: The practical analysis of a dataset in a phylogenetic context will have been covered during computer practicals. Students will thus be able to concretely reproduce it on their own datasets;
Applications: The 5-credit declination of this course imposes the student to carry out a quite extensive personal project. This will help him/her to acquire a better mastery of the concepts and of the practical aspects of the phylogenetic analysis (beyond the tools covered during the computer practicals).

Prerequisite knowledge and skills :

The course assumes no prerequisites in computer science, but relies on a basic knowledge of mathematics and molecular genetics. In principle, the necessary level in both subjects is reached at the end of the 3rd year of BA in biology.

Planned learning activities and teaching methods :

Theoretical lectures, demonstrations and supervised exercises: 7 x 3h.
Computer practicals (Seaview and R): 3 x 3h.
Personal project with written report (full phylogenetic study on a topic to be determined).

Mode of delivery (face-to-face ; distance-learning) :

This is a face-to-face course. Attending the lectures is strongly encouraged as they are designed so as to facilitate understanding and assimilation of the course material. The personal project will be organized as an individual coaching.