Product or service

Haploblock Aggregator

Haploblock Aggregator is a software tool that collects segregation configurations of individual genetic markers and uses them to generate aggregate marker scores for an entire multi-marker haploblock. These compressed, more information-dense datasets have a considerably reduced proportion of missing and non-informative data and thereby reduce the computational and conceptual complexity of creating genetic linkage maps on huge numbers of tightly linked SNP markers. Hereby, it improves the quality of integrated genetic linkage maps as generated by down-stream mapping software. In addition, Haploblock Aggregator supports an innovative approach for the generation of integrated linkage maps across multiple families, where the classical Cross-Pollination design is replaced by a pseudo Back Cross design by an automated conversion of the data. Haploblock Aggregator follows the format of JoinMap® input files, and the result can be directly used in mapping.



Haploblock Aggregator was released under the MIT License and is copyright 2015 Wageningen UR. Click on the link to the zip file on this page to download Haploblock Aggregator. For installation, extract the zip-file to a folder on your computer, and start HaploblockAggregator.exe.


Haploblock Aggregator was developed by Johannes W. Kruisselbrink (Wageningen UR Biometris), Erica Adele Di Pierro (Department of Biosciences, University of Milan), Marco C.A.M. Bink (Wageningen UR Biometris), Luca Gianfranceschi (Department of Biosciences, University of Milan), and Eric van de Weg (Wageningen UR Plant Breeding).

When using Haploblock Aggregator, please reference:

Johannes W. Kruisselbrink, Erica Adele Di Pierro, Luca Gianfranceschi, Marco C.A.M. Bink, and W. Eric van de Weg, 2016, Haploblock Aggregator: combining segregation patterns of consecutive SNP markers into haploblock segregation patterns for generating integrated genetic linkage maps.


This work was co-funded by the EU Seventh Framework Programme by the FruitBreedomics project nr. 265582: Integrated Approach for increasing breeding efficiency in fruit tree crops. The views expressed in this work are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission.