
Slides day 1
Exercise 1  Parameter estimation
Exercise 2  Tree topologies
Exercise 3  Model comparison
Exercise 4  Branch support
Exercise 5  Command line
Exercise 6  Inferring ML phylogenies with codon models
Exercise 7  Inferring ML phylogenies using real datasets
Exercise 8  ReAnalyze published datasets
Exercise 3  Model comparison
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 substitution models the final inferred tree topology.
In this exercise you are asked to infer the phylogenetic tree on the same dataset using different substitution models (and their variations). Use now GTR+Gamma and JC+Gamma, GTR, HKY and JC.
First Run
Run PhyML with the substitution model set to GTR, estimating the nucleotide frequencies empirically from the dataset, and executing the tree search optimisation routines.
In addition, set the following options:
 Gamma distribution with 4 classes
 Estimating Gamma shape parameter
 Adding Invariable sites option
 Gamma distribution with 4 classes
 Estimating Gamma shape parameter
 Adding Invariable sites option
Second Run
Run PhyML with the substitution model set to HKY, estimating the transition/transversion ratio, estimating the nucleotide frequencies empirically from the dataset, and executing the tree search optimisation routines.
In addition, set the following options:
 Gamma distribution with 4 classes
 Estimating Gamma shape parameter
 Adding Invariable sites option
 Gamma distribution with 4 classes
 Estimating Gamma shape parameter
 Adding Invariable sites option
Third Run
Run PhyML with the substitution model set to JC and executing the tree search routines.
In addition, set the following options:
 Gamma distribution with 4 classes
 Estimating Gamma shape parameter
 Adding Invariable sites option
 Gamma distribution with 4 classes
 Estimating Gamma shape parameter
 Adding Invariable sites option
 Which model is the best (including HKY+Gamma), based on the AIC criterion?
 What about adding invariant sites (+I)?
This exercise was prepared by Maria Anisimova
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