In the GUI you trigger the computation of a Project via a manual click on the Start button, on the Computation tab. In order to be able to truly automate the bulk of Amplicon Variant Analysis, you need a way to trigger computation independently of manual GUI interaction. The CLI has a set of “computation” commands (see section 3.4.3 for the usage statement) that allow you to control Project computation from the doAmplicon command interpreter, freeing you from GUI interaction through the computation stage.