Using consensus

The consensus program is used to exploit the large sample of states produced by mcmcphase. The program still lacks the ability to produce a consensus tree by itself and requires that tree from the user. Many phylogenetic programs can build a consensus tree from the sample of topologies produced by mcmcphase in the ``.samples'' file. You can use the consense program of PHYLIP for instance. To use consensus, simply type at the command-line:
consensus mcmcphase-control-file consensus-topology-file
where mcmcphase-control-file is the control file that was used by the mcmcphase program to produce the results and consensus-topology-file is the file which contains the consensus topology. Since mcmcphase outputs the topologies using numbers instead of the names of the species, consensus expects the consensus topology to be given with numbers too.

The consensus program retrieves the model used and the location of the sample files from the control-file. Two consensus substitution models are produced using respectively the mean and median values of the sample. The consensus topology is used to produce a consensus tree with branch lengths. The branch lengths of the states whose topology is identical to the consensus topology are used. For each branch, the consensus length is simply the mean value of all the lengths. The consensus program cannot return a consensus tree if the consensus topology has never been visited. In such a case, we suggest you use optimise to produce ML branch lengths.