Using mcmcphase

The mcmcphase program perfoms Bayesian estimation of phylogenies and uses Markov chain Monte Carlo to produce large samples from the posterior probability density. To use mcmcphase, simply type at the command-line:
mcmcphase mcmcphase-control-file
where mcmcphase-control-file is a valid control file for the mcmcphase program.

The mcmcphase program saves the results of an inference in many files. Be warned that it might require a large amount of disk space for large studies (around 90 Mb for 70 species and 50000 samples).

.besttree and .bestmodel files:

the phylogeny and the parameters of the substitution model when the best state (i.e., the state with the highest likelihood) was visited, it is not necessary one of the sampled configurations and this state might have been visited during the burnin period. The best configuration is not very important in a MCMC analysis but a ``strange'' best state indicates quickly that something went wrong. The tree and the model can also be used as starting points in maximum likelihood inference.

.mp file:

the file with the sampled parameters of the substitution model(s). Each sample occupies one line. The parameters are, in order,

the proportion of invariant sites if an invariant category is used (+I models)

the gamma shape parameter ($\alpha$) if the discrete gamma model is used (+dGX models)

the frequencies of the states as they appear in the substitution matrix

the rate ratios

When a MIXED model is used, substitution model parameters are printed sequentially. Except for the first model, each set of parameters is preceded by the average substitution rate of the model. The average substitution rate for the first model is always 1.0 and therefore this value is not reported.

.samples file: the sampled topologies, this file can be used with another phylogenetic package to produce a consensus tree. To avoid wasting disk space, mcmcphase will output the sampled topologies using an index for each species according to their appearance order in the datafile.

.bl file: the branch lengths for the previous topologies (for use with other PHASE programs).

.output file: a file with similar content to the screen output.

.plot file: the evolution of the likelihood during the run. Sampling of these values starts at the beginning of the run, i.e., likelihood values are stored durning the burnin too.