MEGA-CC Overview

Description

MEGA-CC is the command-line interface for using MEGA and it is included with the graphical interface (GUI). Most of the calculations that are available in the graphical interface (MEGA-GUI) are also available in MEGA-CC. However, all calculation results are saved to files on your computer instead of being displayed using graphical tools. With MEGA-CC, you can batch process data files, automate calculation workflows, and integrate MEGA into analysis pipelines.

MEGA-CC Input Data Files

In order to run MEGA-CC, a minimum of two input files are required - a MEGA Analysis Options (.mao) file and one or more data files that are to be analyzed:

MEGA Analysis Options file

Specifies the calculation and desired settings.
Created using MEGA-GUI.
Has a .mao file extension.

Data file (one or more of the following)

Multiple sequence alignment in MEGA or Fasta format.
Distance matrix in MEGA format.
Unaligned sequences in Fasta format (for sequence alignment only).
Newick tree file (required for some analyses)
Calibrations file (for timetree analysis – but it’s optional)
Groups file (required for timetree analysis, optional for some other analyses)

MEGA-CC Output Files

All results produced by MEGA-CC are written to files on your computer:

In general, two kinds of output files are produced

Calculation-specific results file (Newick file, distance matrix,…).
A summary file with additional info (likelihood, SBL,…).

Some analyses produce additional output (bootstrap consensus tree, csv files, etc…).
Output directory/filename

Default is the same location as the input data file.
Specify an output directory and/or file name using -o option.
If no output filename is specified, MEGA-CC will assign a unique name.

Errors/warnings

If MEGA-CC produces any errors or warnings, they will be logged in the summary file.

Generating a MEGA Analysis Options file

Set MEGA-GUI to Prototype mode by clicking the Prototype button on the main form
Specify a data type that will be used by selecting from a drop-down list
Select an analysis to run from one of the menus on the main form
Select analysis options in the Analysis Preferences Dialog
Click the Save Settings button and save to the .mao file to your computer (most likely in the same directory as the data files to be analyzed)

Running MEGA-CC

There are multiple ways in which MEGA-CC can be used:

Easiest to run using command-line or batch scripts:

megacc –a settings.mao –d alignment.meg –o outFile

Can also be run using custom scripts (Perl, Python, …):

exec(‘megacc –a options.mao –d alignment.meg –o outFile’);

Integrated File Iterator system can process multiple files without the need for using scripts (see Demo2 below)
In addition, other applications can launch MEGA-CC:

status = CreateProcess(“path/to/megacc…”);

To see a list of available command options, call megacc from a command-line prompt with the –h flag (Unix users can view the man page).