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.

PhyML News


A new PhyML release is now available: PhyML 3.1
March 2013
See the Downloads section

A new beta version of PhyML is now available
October 2011
See the Downloads section

PhyML 3.0 is now available
May 2008

PhyML publication becomes a "Current Classic" paper
April 2008
Science Watch

Publication
March 2008
"An Improved General Amino-Acid Replacement Matrix."
Le S.Q., Gascuel O.
Molecular Biology and Evolution. 25(7):1307-20.

PhyML reaches 1000 citations
February 2008

Publication
August 2006
"Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative."
Anisimova M., Gascuel O.
Systematic Biology. 55(4):539-552

Publication
December 2005
"Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood."
Hordijk W., Gascuel O.
Bioinformatics 21(24), 4338-4347

PhyML is presented in the CNRS international magazine
See the article

PhyML publication becomes a "Fast Breaking" paper
February 2005
Science Citation Index article