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.