PhyML is a software that estimates maximum likelihood phylogenies
from alignments of nucleotide or amino acid sequences. It provides a
wide range of options that were designed to facilitate standard
phylogenetic analyses. The main strengths of PhyML lies in the large
number of substitution models coupled to various options to search
the space of phylogenetic tree topologies, going from very fast and
efficient methods to slower but generally more accurate approaches.
It also implements two methods to evaluate branch supports in a sound
statistical framework (the non-parametric bootstrap and the
approximate likelihood ratio test).

NOTE 1: This also builds Phyrex and the MPI (using multiple processors)
version of PhyML. The executable of the latter is called phyml-mpi and
requires openmpi. If you do not want them to be built in the package,
check the SlackBuild script.

NOTE 2: PhyTime used to be part of the PhyML package. However, PhyTime
from the latest releases of PhyML does not build anymore. meanwhile,
PhyTime is available separately, which installs the latest version that
builds.

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.