Aims

The course will provide basic knowledge in modern theories for phylogenetic inference and evaluation, and how phylogenies can be used to solve biological problems. The course also gives basic skills in phylogenetic analysis, with focus on DNA sequence data.

Content

Phylogenetic trees and other models. Optimality criteria for selecting hypothesis; parsimony, maximum likelihood, methods based on pair-wise distances. Substitution models for DNA and other data types. Super trees, consensus trees, compatibility betweeen trees. Algorithms for evaluating tree space; rearrangements, Markov Chain Monte Carlo, genetic algorithms. Evaluating results from phylogenetic analyses; resampling and permutations, tree shape. Coalescens, recombination, horisontal gene transfer. Comparative methods.

Assessment

Written exam at the end of the course. To pass the course, computer assignments/exercises as well as hand-in assignments must have been approved.