Phylogenetic Analysis by Maximum Likelihood (PAML)

 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.