paml 4.4e-1 (amd64 binary) in ubuntu quantal

 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.