The AVA-CLI command language consists mainly of a set of commands to create, modify, and associate Project entities and to perform, and report the results of, Project computations. Additional commands exist for Project validation, data export, and setting the behavior of the doAmplicon command interpreter itself, to assist in debugging problems in CLI scripts. The commands and their command option specifier are all case-insensitive. The Project entities that can be created or manipulated, and their associated commands, are listed below. The usage statement for the doAmplicon command interpreter itself is in section 3.3.2.1. Help information that applies generally to the command language is presented in section 3.3. Detailed usage statements for individual commands are listed in section 3.4, providing a Reference Guide to the command language. Section 3.5 provides a more high-level overview of the language, including a full example script to create a new Project in section 3.5.15. Finally, another (more limited) example script is provided in section 3.6, to display some of the particular features of MID-based Projects.