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

"SMS: Smart Model Selection in PhyML."
Vincent Lefort, Jean-Emmanuel Longueville, Olivier Gascuel.
Molecular Biology and Evolution, 34(9):2422-2424, 2017.

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