Phylogenomics and selection pressure

Phylogenomics and selection pressure (16/08/2016)

This training session is organized by the bios4Biol CATI and the Genotoul bioinfo platform and aims at initiating participants to molecular phylogenetics studies. The morning course will provide insights about sampling problems in phylogenomics studies (genes, species) and methodological aspects of phylogenomics studies with two major focus on super-matrix and super-tree methods. The afternoon course will be dedicated to the use of the PAML4 package in order to study selection pressures in a sequence alignment.

 

This training focuses on practice. It consists of four modules with a large variety of exercises described hereunder:

• Build the dataset (09:00 am to 10:00 am): What scale for infering species phylogeny? Orthology inference.
• Phylogenomics analysis (10:00 am to 12:00 pm): Whole genome features methods, sequence based approach (supermatrix and supertree).
• How to compare trees and conclusion (12:00 pm to 12:30 pm)
• Planning under construction (14:00 pm to 17:00 pm)

The session will take place the room ‘salle de formation’ at INRA center of Toulouse-Auzeville.

Prerequisites: ability to use a Unix environment (see Unix training) and knowledge of the sequence alignment (see Sequence alignment training), evolutionary models and the phylogenetic inference methods (see methods for phylogenetic trees construction training. Training materials will be available on the website before the session. Slides in a “taking notes” format will be downloadable from our web site. A Unix reference command leaflet will also be provided. Only the latter will be available during the session.

  Phylogenomics training slides and data for the exercises. Selection Pressure training slides and data for the exercises.

Bookings: Phylogenomics and selection pressure