Phylogenetic trees

David H. Ardell

Linnaeus Centre for Bioinformatics, Box 598, 751 24 Uppsala, Sweden

Abstract:

In this tutorial you will learn different ways trees are repesented, then you will do an exercise to understand maximum parsimony principle. Then you will start making trees. First you will look at the affect of alignment on trees made with parsimony. Then you evolve some trees with long branches and see that model-based methods (maximum likelihood) often works better than parsimony when some taxa have evolved significant distances. Last you will practice applying the bootstrap to make a neighbor-joining tree.