Information about software packages installed on the ICHEC systems.
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.
The copyright for PhyML is held by CNRS - Universite Montpellier II. Please refer to http://www.atgc-montpellier.fr/phyml/binaries.php for full copyright details.
To use PhyML, load the relevant environment module:
Further information can be obtained from http://atgc.lirmm.fr/phyml/.
How to cite PhyML:
Guindon S. and Gascuel O. (2003)
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
Systematic Biology 52(5): 696-704.