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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 - Re-Analyze published datasets
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
Tasks
- Write down command lines to execute the analyses performed in (1)-(4).
This exercise was prepared by Maria Anisimova