Mega2 Bitbucket repository

The latest development snapshot of the Mega2 code can be obtained from this Bitbucket repository. Please note that this development snapshot is not as thoroughly tested as our stable release version, but does contain the newest features and changes.

To obtain the stable release version (including pre-compiled binaries), please go to http://watson.hgen.pitt.edu/register.


Please see the Mega2 documentation, which is available in this distribution as a PDF in the mega2_html folder:


It is also available online as html http://watson.hgen.pitt.edu/docs/mega2_html/mega2.html and as a pdf http://watson.hgen.pitt.edu/docs/mega2_html/Mega2_Documentation.pdf.

Mega2 Releases

4.7.0 -- Mega2 now passes non-numeric alleles through (without recoding them to numeric alleles) to analysis programs that will accept non-numeric alleles.

4.6.3 -- fixes a bug in PLINK format introduced by 4.6.2

4.6.2 -- adds VCF (Variant Call Format) to Mega2

4.6.1 -- generates PLINK/SEQ output; adds support for native and MINGW Windows 8

4.6.0 -- improves memory efficency: 2 bits for markers with two allele

A note about Mega2 versions available via git:

  • The master branch reflects our latest working code; it may contain bugs.

  • The current stable release is named v4.7.0_Release; you should "git checkout v4.7.0_Release" after cloning Mega2. Alternatively, you can download source code for the stable release by clicking on 'Downloads' and then on 'Tags'.