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.

Gowri-Shankar Vivek 2003-04-24