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HaploPOP software

HaploPOP is a software to build informative haplotypes for population genetic structure inference.


Population assignment uses genetic information to assign individuals to predefined populations. There are diverse applications of assignment methods in ecology and human forensics. However, assigning individuals to populations can be difficult when the level of genetic differentiation between populations is too small. haplopop combines markers into haplotypes to improve the accuracy of population assignment. The software uses the Gain of Informativeness for Assignement statistic that provides a criterion to decide whether markers should be combined into haplotypes. Because there is a combinatorial problem that arises when constructing haplotypes with large number of molecular markers, haplopop can construct haplotypes within genomic windows of fixed sizes.
Figure on the left: Mean Incorrect Assignment as a function of window size (in kbp). Study is done using 3-population divergence model, with various recombination rates.

Download the latest version of HaploPOP (April 2013)

  • Download for Windows (Available soon): HaploPOP.exe

  • Download for UNIX type OS: HaploPOP1.0.tar.gz

  • Manual


    • Duforet-Frebourg N., Gattepaille L.M., Blum M.G.B and Jakobsson M. Haplopop: a software that improves population assignment by combining markers into haplotypes. (in prep)
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