PAML (Phylogenetic Analysis Using Maximum Likelihood) is a package of programs for maximum likelihood analysis of protein and DNA sequences (Yang 1997). PAML is useful if you are interested in the process of sequence evolution. The two main programs, baseml and codeml, implement a number of sophisticated models, which you can use to construct likelihood ratio tests of evolutionary hypotheses.
All programs in the PAML package have control files that specify the name of the sequence data file, the tree structure file, and models and options for the analysis (these may be recognized by the *.ctl extension). To run any of these programs, either type
baseml, basemlg, evolver, or yn00 at a terminal window prompt. The only exception is for the programs codonml and aaml which are both run under the command:
codeml
Running any of the programs requires a sequence data file, a tree file (in Newick format – optional in some programs) and the appropriate control file before running the programs. Note that the control file should be modified to fit your type of analysis. The formats of data files and tree files are detailed in the package documentation.