Epistasis Tools is a collection of efficient programs for epistasis detection in genome-wide data. With user-provided genotype and phenotype data, as well as a few parameters, the programs are able to return the significant SNP-pairs. The programs are implementations of efficient epistasis detection algorithms, which greatly speed up the computationally intensive process.

Currently, the collection consists of three main programs: FastANOVA[paper], COE[paper], and TEAM[paper]. The three programs are suitable for different problem settings. Please refer to the following table for the setting that is suitable for each program.

Algorithm	Genotype	Phenotype	Error Type	Sample Size	Supported Test
FastANOVA	homozygous	quantitative	FWER	less than a hundred	ANOVA test
COE	homozygous	binary	FWER	less than a hundred	convex tests
TEAM	heterozygous	binary	FWER & FDR	hundreds of thousands	tests based on contingency tables

Besides source code(link), we also provide a web-interface for the applications. To use the applications online, users need to follow the listed steps.

(1) Register a user name in Registration
(2) Select an application on the left panel
(3) Upload the datasets and set the parameters
(4) Click the [Submit] button
(5) Monitor the status and get the result in Progress Monitor

Please note that the size limit of the uploaded dataset is 3 Megabytes. For analysis that involves large or sensitive datasets, it is recommended to download and run the programs.