PAML: Phylogenetic Analysis by Maximum Likelihood

PAML is a package of programs for phylogenetic analyses of DNA or
protein sequences using maximum likelihood. PAML is not good for tree
making. It may be used to estimate parameters and test hypotheses to
study the evolutionary process, when you have reconstructed trees
using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.

This is pamlX: the graphical user interface for PAML.