How to use PhyML

Getting started with PhyML

1. Download the software

2. Launch
  • 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. PhyML-3.1_linux64)


  • 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 Terminal).

3. Interface

PhyML allows the user to prepare the analysis with two different interfaces:

  • Menu: this interface will be loaded once the user provides a valid alignment file
    (WARN: remember the difference between interleaved and sequential files).

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You can move between menus using the + and - key on your keyboard and pressing enter to 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:

m + enter | The model will be changed into F84
m + enter | The model will be changed into TN93
m + enter | The model will be changed into GTR

The same procedure applies for all the other commands.

  • Command Line: this interface allows the user to set all the configuration parameters in one single step, dynamically but not interactively.

You an find more informations here:


  1. PhyML, a tool for biologists