Inferring the evolutionary relationships between different living species, we can compare their genomes and protein sequences using PhyML.
1. Download the software
PhyML runs without a graphical user interface (GUI). Therefore, you will see a black terminal window appearing on your monitor anytime you execute it.
WARN: On Windows machines
PhyML will close automatically the terminal session at the end of the execution.
PhyML execution can be started either with:
- a double click on PhyML-3.1_your-operative-system (i.e.
- dragging PhyML-3.1_your-operative-system (i.e.
PhyML-3.1_linux64) into a new terminal session (on OsX and Linux operative systems search for
PhyML allows the user to prepare the analysis with two different interfaces:
You can move between menus using the
-key on your keyboard and pressing
enterto confirm the command.
To modify a command (i.e. modify the substitution model from the default to GTR):
[M] ................. Model of nucleotide substitution HKY85
you need to press the following sequence of keys on your keyboard:
enter| The model will be changed into F84
enter| The model will be changed into TN93
enter| The model will be changed into GTR
The same procedure applies for all the other commands.
You an find more informations here:
Document last updated on 10.02.2016
© 2016 Lorenzo Gatti – Applied Computational Genomic Team (ACGT) @ Institute of Applied Simulations (ZHAW) | Wädenswil | Zürich