codeml - phylogenetic analyses of DNA or protein sequences using maximum likelihood

http://nebc.nerc.ac.uk/bioinformatics/docs/codeml.html


codeml is a part of the PAML package, which is a suite of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood (ML).

With the seqtype set to 1, codeml carries out ML analysis of protein-coding DNA sequences using codon substitution models (e.g., Goldman and Yang 1994). With seqtype set to 2, codeml carries out ML analysis of amino acid sequences under a number of amino acid substitution models.