Exercise 5 - Command line

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: Using PhyML from the command line

Discover the specification of PhyML options on a command line by typing phyml -h. W

  1. Write down command lines to execute the analyses performed in (1)-(4). 

This exercise was prepared by Maria Anisimova