Exercise 7 - Inferring ML phylogenies using real datasets

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: Analysing real datasets

Analyze a real dataset - the primate AA dataset - and test for substitution models with and without frequencies estimation.

Datasets
Dataset file:
primates-aa.phy

Fist Step

Set the model to LG+Gamma, and try both +F and –F options.

Second Step

Search for the best model using ProtTest: http://darwin.uvigo.es/software/prottest2_server.html

Tasks
  1. Compare the trees and the likelihood values. Which model is best, based on AIC criterion. What about using invariant sites?
  2. After executing the second step, compare the trees, likelihood and AIC values to those of LG+Gamma. 


This exercise was prepared by Maria Anisimova