PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained by Ziheng Yang and distributed under the GNU GPL v3. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. 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.