ATGC: PhyML

PhyML 3.0: new algorithms, methods and utilities

Please cite:
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood."

Guindon S., Gascuel O.

Systematic Biology, 52(5):696-704, 2003.

Paper

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, in press, 2010.

Related papers

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" .

Contacts

For any question about the algorithm, the program options or the source code, please contact:

Stéphane Guindon (author)
LIRMM, Montpellier, France.
Olivier Gascuel (author)
LIRMM, Montpellier, France.
Jean-François Dufayard (programer)
LIRMM, Montpellier, France.
Vincent Lefort (web master)
LIRMM, Montpellier, France.