PhyML-3.1 (released in 2012):

• PhyML-3.1 (zip archive).
  This version of PhyML implements aBayes branches support algorithm and corrects several minor bugs.
  This release is obtained from the source code version 20120112 patched with the 20121208 patch.

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Supplementary versions

• PhyML-structureThis version of PhyML implements the structure based models described in:« Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics is Highly Beneficial. »Le S.Q., Gascuel O.Systematic Biology, 59(3):277-87, 2010.
• PhyML-CATThis version of PhyML implements the CAT model described in:« Empirical profile mixture models for phylogenetic reconstruction. »Le S.Q., Gascuel O., Lartillot N.Bioinformatics, 24(20):2317-23, 2008.
• PhyML-mixtureThis version of PhyML implements the mixture models described in:« Phylogenetic Mixture Models for Proteins. »Le S.Q., Lartillot N., Gascuel O.Philosophical Transactions of the Royal Society B, 363(1512):3965-76, 2008.

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Previous versions

These versions of PhyML contain some bugs which were corrected into the PhyML 3.0 version.
PhyML 3.0 was also greatly optimized and provides new functionalities.

• PhyML-v2.4.4 (tar.gz archive).
  This is the original version of PhyML:« A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. »Guindon S., Gascuel O.Systematic Biology, 52(5):696-704, 2003.
• PhyML-SPRThis version of PhyML implements the algorithm described in:« 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-aLRTThis version of PhyML implements the algorithm described in:« Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative. »Anisimova M., Gascuel O.Systematic Biology, 55(4), 539-552, 2006.
• PhyML-aBayes (beta version) (zip archive).
  This version of PhyML implements aBayes branches support algorithm described in:« 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.

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Unofficial versions

• PhyMLratesThis version of PhyML implements the algorithm described in: »Calculating the Evolutionary Rates of Different Genes: A Fast, Accurate Estimator with Applications to Maximum Likelihood Phylogenetic Analysis. »Rachel BevanSystematic Biology. 2005 54(6):900-915.Download C source code (tar.gz archive).
  Contact: rachel@mcb.macgill.ca, McGill Centre for Bioinformatics, Montreal, Quebec, Canada.
• PhyML – MPIThis is a parallel version of PhyML. It only works when the bootstrap option is on.Martha TorresDownload C source code (tar.gz archive).
  Contact: mxtd@uesc.br, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil.
• nhPhyMLThis version of PhyML implements the algorithm described in: »Efficient likelihood computations with nonreversible models of evolution. »Bastien Boussau, Manolo GouySystematic Biology. 2006 55(5):756-68.This is a program built to compute phylogenetic trees under the non stationary, non homogeneous model of Galtier and Gouy (1998). As such, it provides estimates of the G+C contents of ancient sequences. It uses the algorithmic structure of PhyML adapted to the rooted and irreversible case. Download C source code (tar.gz archive).
  Contact: boussau@biomserv.univ-lyon1.fr, Université Claude Bernard, Lyon, France. http://pbil.univ-lyon1.fr/software/nhphyml/