PhyML 3.0: new algorithms, methods and utilities

Please cite:
"New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0."
Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O.
Systematic Biology, 59(3):307-21, 2010.

PhyML is available on GitHub.


PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology. Since the original publication (Guindon and Gascuel 2003), PhyML has been widely used (>1,250 citations in ISI Web of Science), due to its simplicity and a fair accuracy/speed compromise. In the mean time research around PhyML has continued. We designed an efficient algorithm to search the tree space using Subtree Pruning and Regrafting (SPR) topological moves (Hordijk and Gascuel 2005), and proposed a fast branch test based on an approximate likelihood ratio test (Anisimova and Gascuel 2006). However, these novelties were not included in the official version of PhyML, and we found that improvements were still needed in order to make them effective in some practical cases. PhyML 3.0 achieves this task. It implements new algorithms to search the space of tree topologies with user-defined intensity. A non-parametric, Shimodaira-Hasegawa-like branch test is also available. The program provides a number of new evolutionary models and its interface was entirely re-designed. We tested PhyML 3.0 on a large collection of real data sets to ensure that the new version is stable, ready-to-use and still reasonably fast and accurate.

User guide

More explanations are given in the PhyML manual.
Online interface PHYLIP-like interface Command-line interface

The online interface

It is a web form that you fill with your values for the program options, your name and your email; then click on the "Execute & email results" button to start the program with your settings; after a while you will receive your results at the email address that you provided. Note that you can also ask to be notified by email of the program developments by subscribing to the mailing list.

PhyML online interface

For a quick start, simply select the "Example" radio button, type your name, country where you are and email, and click the "Execute & email results" button. This will run the program with default values; the example sequence file contains 5 DNA data sets in PHYLIP sequential format with 60 taxa and 500 bp sequences.


PhyML produces several results files: Here are the possible uses of PhyML: