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PhyML is a phylogeny software based on the maximum-likelihood
principle. Early PhyML versions used a fast algorithm to perform
Nearest Neighbor Interchanges (NNIs), in order to improve a
reasonable starting tree topology.
For details and citation
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.
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