Phylogenetic Analysis by Maximum Likelihood (PAML)

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

WWW: http://abacus.gene.ucl.ac.uk/software/paml.html