The Bio++ Program Suite is a package of programs using the Bio++ libraries and dedicated to Phylogenetics and Molecular Evolution. All programs are independent, but can be combined to perform rather complex analyses. These programs use the interface helper tools of the libraries, and hence share the same syntax. They also have several options in common, which may also be shared by third-party software. This manual was hence split into three parts:
A general description of the language used to interact with the programs.
A more detailed description about several options that are encountered in several programs. This includes input/output of data and model specifications.
Include a reference of all available options for each program in the package.