An algorithm for multiple quantitative trait locus (QTL) scan with epistatic interactions. PruneDIRECT algorithm has specific strengths for permutation testing. It has been integrated to a flexible, parallel computing framework for identifying multiple interacting QTL which uses the map-reduce model as implemented in Hadoop. This framework is implemented in R, a widely used software tool among geneticists. This enables users to rearrange algorithmic steps to adapt genetic models, search algorithms, and parallelization steps to their needs in a flexible way.