PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
A summary of the types of analyses performed by different programs: baseml: ML analysis of nucleotide sequences basemlg: ML analysis of nucleotide sequences under the model of gamma rates among sites. codonml (codeml with seqtype = 1): ML analysis of protein-coding DNA sequences aaml (codeml with seqtype = 2): ML analysis of amino acid sequences under a number of amino acid substitution models pamp: Parsimony-based analyses for a given tree topology mcmctree: Bayesian estimation of phylogenies using DNA sequence data evolver: This program used to be named listtree yn00: estimating synonymous and nonsynonymous substitution rates in pairwise comparison of protein-coding DNA sequences.
Please refer to PAML for more details.
Most programs in the PAML package have control files that specify the names of the sequence data file, the tree structure file, and models and options for the analysis. The default control files are baseml.ctl for baseml and basemlg, codeml.ctl for codeml, pamp.ctl for pamp, mcmctree.ctl for mcmctree. The progam evolver does not have a control file, and uses a simple user interface. All you do is to type evolver and then choose the options. For other programs, you should prepare a sequence data file and a tree structure file, and modify the appropriate control files before running the programs. The formats of those files are detailed in the documentation in the package.
You need to prepare a sequence data file (e.g., brown.nuc) and modify the options in the appropriate control file. If you have chosen runmode = 0 or 1 in the control file, which means that the tree topologies are specified, you also need to prepare a tree structure file (e.g., trees.4s). On UNIX or Windows systems, you run the programs from a command prompt by
ProgramName [for example, baseml]
or
ProgramName ControlFileName
Most programs in the PAML package have control files that specify the names of the sequence data file, the tree structure file, and models and options for the analysis. The default control files are baseml.ctl for baseml and basemlg, codeml.ctl for codeml, pamp.ctl for pamp, mcmctree.ctl for mcmctree. The progam evolver does not have a control file, and uses a simple user interface. All you do is to type evolver and then choose the options. For other programs, you should prepare a sequence data file and a tree structure file, and modify the appropriate control files before running the programs. The formats of those files are detailed in the documentation in the package.
You need to prepare a sequence data file (e.g., brown.nuc) and modify the options in the appropriate control file. If you have chosen runmode = 0 or 1 in the control file, which means that the tree topologies are specified, you also need to prepare a tree structure file (e.g., trees.4s). On UNIX or Windows systems, you run the programs from a command prompt by
ProgramName [for example, baseml]
or
ProgramName ControlFileName
e.g.
cp /usr/local/paml/paml-last/*.ctl /usr/local/paml/paml-last/*.trees .
Orbaseml
baseml /usr/local/paml/paml-last/baseml.ctl
baseml control file is at /usr/local/paml/paml-last/baseml.ctl
...
User could substitude the above ctl and trees files with their own ctl file and .trees files