Description of programs in the PHASE package

The PHASE (PHylogenetics and Sequence Evolution) package consists of two main programs, mlphase and mcmcphase.

mlphase performs maximum-likelihood inference

mcmcphase is a Bayesian phylogenetic inference program

There are five other smaller programs in the package:

analyser checks the content of the molecular sequences

likelihood computes the likelihood given a specified evolution model

simulate generates sequences according to a specified evolution model

optimise is a smaller version of mlphase without tree search capabilities

consensus is used with mcmcphase to summarize the results of a MCMC run.

Below we summarize the behaviour of these programs. Please refer to the first chapter in order to learn how to use them.