JZmapqtl is part of the QTL Cartographer suite of programs.

JZmapqtl uses (composite) interval mapping to map quantitative trait loci to a map of molecular markers and can analyze multiple traits simultaneously. It requires a molecular map that could be a random one produced by Rmap, or a real one in the same format as the output of Rmap.

In addition, the program requires the results of the stepwise linear regression analysis of SRmapqtl for composite interval mapping.