PhyML with Smart Model Selection. SMS can also be used on its own.

Please cite:
"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.

PhyML is available on GitHub.

How it works

Source code

SMS tests on 500 DNA and 500 protein MSA

SMS tests on 50 DNA and 50 protein MSA

Data sets