Institute of Fruit Tree and Tea Science, NARO

Minimal Marker

The computer program, Minimal Marker, can identify all the appropriate minimal marker set(s) for a given variety/marker type table using a co-dominant marker set or dominant marker set. In many cases of using DNA markers, it is unnecessary to use all of the markers listed in a variety/marker type table to discriminate all of the varieties of a crop. If a minimal marker set (which is the minimal number of a marker set that can discriminate all varieties in a particular variety/marker type table) is established by MinimalMarker, one can discriminate varieties efficiently in terms of both labor and time.

System requirement

Minimal Marker runs in the execution environment of Perl, such as Windows, Mac OS X, and Linux. In case of Windows machine, you have to install Perl environment such as ActivePerl (


MinimalMarker provided by Agriculture and Food Research Organization (NARO) may be freely distributed, provided that no charge above the cost of distribution is levied, and that the disclaimer below is always attached to it.

MinimalMarker is provided as is without any guarantees or warranty. Although the author has attempted to find and correct any bugs in the program on MinimalMarker, the author is not responsible for any damage or losses of any kind caused by the use or misuse of MinimalMarker. The author is under no obligation to provide support, service, corrections, or upgrades of MinimalMarker.

Copy right

The computer program on MinimalMarker is protected by copyright. Except as specifically permitted, no portion of this software may be distributed or reproduced by any means, or in any form, without NARO's prior written permission.

© 2006-2019 NARO, Japan. All rights reserved.


When publishing an academic paper using the results obtained using the MinimalMarker, please describe the use of MinimalMaker in the paper and cite the following literature.

Fujii H., T. Ogata, T. Shimada, T. Endo, H. Iketani, T. Shimizu, T. Yamamoto and M. Omura (2013) Minimal marker: an algorithm and computer program for the identification of minimal sets of discriminating DNA markers for efficient variety identification. Journal of Bioinformatics and Computational Biology 11(2):1250022. DOI: 10.1142/S0219720012500229

Install the software

  • Identify the path to the Perl execution environment
  • Download the software from the following URL
  • Software is compressed by ZIP format.
  • Please download the MinimalMarker by selecting Windows or Mac from the link below.

I want to download "" agree to the disclaimer and copyright policy software.【ZIP:7.7MB】

I want to download "" agree to the disclaimer and copyright policy software.【ZIP:514.6KB】