Exercise 2 - Tree topologies

Inferring phylogenies using maximum likelihood

In this tutorial you will be guided in using PhyML and its extension, CodonPhyML, to solve common phylogenetic problems. For some of the following exercises there might be more than one single solution.

Goal: Observing the effect of tree search routines on the initial inferred tree topology.

In this exercise you are asked to optimise the tree topology on the substitution parameters obtained using ML performing a tree search (i.e. NNI, SPR, TBR) on the initial tree topology.

Datasets
Dataset file:
primates-nt.phy

By default PhyML builds a BioNJ tree and uses this tree as a starting tree. Run PhyML without the tree-search, so that all model parameters are optimized on the BioNJ tree.

Tasks
  1. Compare the ML and the BioNJ trees and the model estimates (HKY+Gamma) obtained for the two trees.
  2. Compare the likelihood of the ML and BioNJ trees.
  3. What do you observe and why?

phylogenies tree-estimation maximum-likelihood parameter-estimation

This exercise was prepared by Maria Anisimova