A web server-based tool for analysing polygenic epistatic effects. PEPIS is based on a linear mixed model that has been used to predict the performance of hybrid rice. It includes two main sub-pipelines: the first for kinship matrix calculation, and the second for polygenic component analyses and genome scanning for main and epistatic effects. PEPIS was dedicatedly developed for epistatic genetic estimation. It will help overcome the bottleneck in genetic epistasis analysis.