SlackBuildsOrg/academic/PhyML

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).

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.