This program is also called megacc, the "cc" standing for "Computational Core"
A preparatory step is required for the configuration of the analysis, facilitated by the program megaproto. This is done via a Graphical User Interface. It produces a mao file which must then be fed to the main megacc program via the -a option.
A main run of the progra is as follows:
megacc -a reltime_ml_nucleotide.mao -d Examples/mtCDNA.meg -t Examples/mtCDNA.nwk -g groups.txt -c Examples/mtCDNACalibration.txt -o timetree.demo