iPat: Interface of Prediction and Association Tools for Genomics

The advances of sequencing technologies brought two areas of rapid developments, one is genome wide association studies and the other is prediction of phenotypes from genotypes. Both areas require sophisticated statistical models. Multiple packages were developed to perform such analyses, including TASSEL, PLINK, rrBLUP, GAPIT, GenABEL, MLMM, FarmCPU and BLINK. Most of these packages, except TASSEL, use command line interface (CLI) to realize the optimum efficiency. These packages require substantial of training on DOS command or R language, which eliminating many users who are comfortable only with graphic user interface (GUI).

The software iPat was developed for such need to transform existing CLI packages such as GAPIT, rrBLUP, and FarmCPU, into a graphic user interface without the compromise on efficiency. With iPat, users can perform analyses by simply clicking mousses to link existing data files, select models, and define input parameters. iPat was developed in Java to use the cutting edge technologies for programming across languages such as Java, C and R. Additional benefit include that iPat can be run on any operating systems including Windows and Mac. The executable file of iPat can be freely download from http://ZZLab.Net/iPat. The website also contains user manual, tutorials and demonstration dataset.