Phylogenetic Analysis by Maximum Likelihood (PAML)

PAML is a program package for phylogenetic analyses of DNA or protein
sequences using maximum likelihood, and is maintained and distributed
by Ziheng Yang. 

Possible uses of the programs are:
- Estimation of branch lengths in a phylogenetic tree and parameters
  in the evolutionary model such as the transition/transversion rate
  ratio, the shape parameter of the gamma distribution for variable
  evolutionary rates among sites, and rate parameters for different
  genes;
- Test of hypotheses concerning sequence evolution, such as rate
  constancy and independence among nucleotide or amino acid sites, rate
  constancy among lineages (the molecular clock), and homogeneity of
  evolutionary process in multiple genes;
- Calculation of substitution rates at sites; 
- Reconstruction of ancestral nucleotide or amino acid sequences;
- Simulation of nucleotide, codon, and amino acid sequence data sets; 
- Phylogenetic tree reconstruction by maximum likelihood and Bayesian methods. 

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