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 » .

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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.