PhyML 3.0: new algorithms, methods and utilities

PhyML is available on GitHub.

Lastest release: PhyML-3.1

• 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.

Supplementary versions

• PhyML-structure
  This 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-CAT
  This 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-mixture
  This 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.

Previous versions

• 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-SPR
  This 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-aLRT
  This 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.

Unofficial versions

• PhyMLrates
  This 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 Bevan
  Systematic 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 - MPI
  This is a parallel version of PhyML. It only works when the bootstrap option is on.
  Martha Torres
  Download C source code (tar.gz archive).
  Contact: mxtd@uesc.br, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil.
• nhPhyML
  This version of PhyML implements the algorithm described in:
  "Efficient likelihood computations with nonreversible models of evolution."
  Bastien Boussau, Manolo Gouy
  Systematic 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/