PhyML 3.0: new algorithms, methods and utilities

New 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 2010 (in press).
• 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.

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/