People with a good background in phylogenetic inference might be interested only in the first chapter which explains how to use PHASE . The second chapter contains a few elements of the theory of phylogenetic inference with some valuable information about PHASE that can make technical details in the first chapter clearer. Experienced phylogeneticists might find it useful to read the RNA substitution models section to learn about RNA substitution models and the Bayesian phylogenetics section if they are not familiar with Markov Chain Monte-Carlo (MCMC) techniques.
Once you have read the short description of the programs in this introduction, you can try them straightaway with the examples provided. However, be warned that inferences using the mammals dataset of 69 species and the maximum likelihood inference with the primates (primates-rna-ml.control) require at least one day. You should use other control files instead.
The first chapter of this manual should be used as a reference only and to clarify obscure points about PHASE programs. The HTML version of these pages is probably more appropriate to find useful information.