Mega2 is a utility program that can be used to convert data files from one format to another. Typically the program can be used to convert Linkage-format files to file-formats used by other programs such as SimWalk2.

It also incorporates analysis functionality, such as test for Hardy-Weinberg equilibrium.

For many of the program options, Mega2 sets up a C-shell script that then can automatically run the appropriate analyses.

Mega2 is structured so that the user proceeds through a series of menus, making choices in each one (or accepting the default values), until the desired output files are created. After the desired output files are created, Mega2 exits.


Version on CSC's Servers

Taito: 5.0.1


Mega2 is an interactive program and best run in Taito-shell. To initialize the program type:

module load biokit

Start the program by typing:


Mega2 is quite simple to use because of its menu-driven interface.




If you use Mega2 as part of a published work, please remember to reference Mega2. You may reference it by citing the following:

Baron RV, Kollar C, Mukhopadhyay N, Weeks DE (2014) Mega2: validated data-reformatting for linkage and association analyses. Source Code for Biology and Medicine 9:26. PubMed PMID: 25687422; PubMed Central PMCID: PMC4269913 DOI: 10.1186/s13029-014-0026-y
as well as citing the web site and the version that you used. For example, the web site citation for version 4.9.2 should be:
Baron RV, Kollar CP, Mukhopadhyay N, Almasy L, Schroeder M, Mulvihill WP, Weeks DE (2015) Mega2 (Version 4.9.2).
Use of Mega2 to convert VCF or BCF input files makes use of a built-in copy of VCFtools; you should cite the following paper:
The Variant Call Format and VCFtools, Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, Bioinformatics (2011) 27 (15): 2156-2158.
Use of Mega2 to convert IMPUTE2 GEN or binary IMPUTE2 BGEN format input files makes use of a built-in copy of bgen; you should also cite the following work:
The BGEN format: A compressed binary format for typed and imputed genotype data,, Gavin Band and Jonathan Marchini