PAML (Phylogenetic Analysis using Maximum Likelihood) is a package of programs for maximum likelihood analysis of protein and DNA sequences. PAML is useful in investigating processes of sequence evolution, not in inferring phylogenies. The two main programs, baseml and codeml, implement a number of sophisticated models, which can be used for the likelihood ratio testing of evolutionary hypotheses.

Using PAML on HPC

PAML programs are launched with their name and a corresponding control file, e.g:

baseml baseml.ctl
codeml codeml.ctl

The control file contains all of the program parameters and needs to be edited to reflect your particular requirements. Some example control files can be found here. Further program documentation is available through the PAML home page, the Workshop on Molecular Evolution, and as a local User's Guide and FAQ.