ATGC: PhyML

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.

Get the latest PhyML releases from GitHub.

Papers

PhyML 3.0:

"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.
SMS:

"SMS: Smart Model Selection in PhyML."

Vincent Lefort, Jean-Emmanuel Longueville, Olivier Gascuel.

Molecular Biology and Evolution, msx149, 2017.

Related papers

aBayes:

"Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes."

Anisimova M., Gil M., Dufayard JF., Dessimoz C. and Gascuel O.

Systematic Biology, 60(5):685-99, 2011.
LG model:

"An Improved General Amino-Acid Replacement Matrix."

Le S.Q., Gascuel O.

Molecular Biology and Evolution, 25(7):1307-20, 2008.
aLRT:

"Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative."

Anisimova M., Gascuel O.

Systematic Biology, 55(4), 539-552, 2006.
SPR:

"Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood."

Hordijk W., Gascuel O.

Bioinformatics, 21(24), pp. 4338-4347, 2005.
PhyML original version:

"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood."

Guindon S., Gascuel O.

Systematic Biology, 52(5):696-704, 2003.

This is a detailed description of the algorithm. This is also a "Fast Breaking Paper" .

Contacts

For any question about the algorithm please contact:

Stéphane Guindon (author)
LIRMM, Montpellier, France.
Olivier Gascuel (author)
LIRMM, Montpellier, France.

The source code and documentation are available on this repository.