How to use Molecular evolutionary Genetic Analysis (MEGA) software

Sophisticated and user-friendly software suite for analyzing DNA and protein sequence data from species and populations.
MEGA can be used with either a graphical user interface (useful for visual exploration of data and results) or a command-line interface (useful for batch or scripted execution). The graphical user interface (GUI) is run in one of two modes. The first mode is the Analyze mode in which all GUI tools in MEGA are enabled and visual results explorers are available for tasks such as editing sequence alignments and viewing phylogenies. This is the mode that most MEGA users are familiar with. The second mode is the Prototype mode which is used solely for generating MEGA Analysis Options (.mao) files that specify analysis settings when using MEGA from a command shell

The command-line interface of MEGA is accessed by opening a command shell and executing the megacc command. The megacc command requires several options, including the path to a .mao file and paths to input data file(s) to be analyzed