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First steps with PhyML

Inferring the evolutionary relationships between different living species, we can compare their genomes and protein sequences using PhyML.

1. Download the software


2. Launch

PhyML execution can be started either with:


3. Interface

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

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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.

You an find more informations here:


  1. PhyML, a tool for biologists http://www2.cnrs.fr/en/454.htm

Document last updated on 10.02.2016

© 2016 Lorenzo Gatti – Applied Computational Genomic Team (ACGT) @ Institute of Applied Simulations (ZHAW) | Wädenswil | Zürich