MEGA-CC is the compute core that is used by MEGA and is installed as a command-line application. This version is useful for iterative and batch analysis of multiple input data files. In order to use MEGA-CC, you first must generate a MEGA Analysis Options (.mao) file which specifies the analysis and settings to run. Then from a command shell, you execute the megacc command, passing parameters for the .mao and input data file(s). See an example here.