Solution 3 - Model comparison

Inferring phylogenies using maximum likelihood

Observing the effect of substitution models the final inferred tree topology.

Goals

In this exercise you are asked to compare different substitution models (and their variations) on the same dataset.

Execution

The number of parameters are computed in the following way for a rooted
tree:

$k = (2 \ast \text{no. taxa} - 3) + \text{no. parameters in substitution model} + \text{extra parameters}$

substitution models: JC = 0 parameters | HKY = 4 parameters | GTR = 8
parameters
invariant sites = +1 parameter
gamma rates = +1 parameter

We compute the AIC value as follows:

$AIC = 2(k) - 2\log(L)$

Questions

1. Which model is the best (including HKY+Gamma), based on the AIC criterion?

We select the model with the lowest AIC value. In this case, GTR + Gamma

This exercise can also be solved using jmodeltest which performs automatically phylogenetic tree reconstructions with every model and extra parameters (i.e. invariant sites, gamma).