The mcmcphase program performs Bayesian phylogenetic inference. It uses a Markov Chain Monte Carlo algorithm to sample from the posterior probability distribution of phylogenetic tree topology, branch lengths and sequence evolution model parameters. For an explanation of Bayesian phylogenetics and a description of the MCMC sampling algorithms used in mcmcphase, please consult the Bayesian Phylogenetics section or Jow et al. (2002).
The consensus program is used to exploit the results of a MCMC run. This program produces two consensus models (using mean and median of the parameters in the sample) and can return consensus branch lengths for any supplied topology, e.g., a PHYLIP-style consensus tree, if similar topologies were sampled during the run.