FastEpistasis statistics

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FastEpistasis specifications


Unique identifier OMICS_10119
Name FastEpistasis
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Parallelization MPI
Computer skills Advanced
Version 2.05
Stability Stable
Maintained Yes


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  • person_outline Thierry Schüpbach <>

Publication for FastEpistasis

FastEpistasis in publications

PMCID: 5943287
PMID: 29426878
DOI: 10.1038/s41437-017-0043-0

[…] iants with p-values for association smaller than 10−3, 10−5, 10−7, and 10−9 to build the additive grm to use in the prediction analysis., we also performed a pairwise interaction gwas (epigwas) using fastepistasis (schüpbach et al. ), testing all possible \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepa […]

PMCID: 4938657
PMID: 27185397
DOI: 10.1534/g3.116.028563

[…] most datasets. we aimed to use data from the resource for genetic epidemiology research on adult health and aging (gera) study to search for snp-snp interactions associated with 10 common diseases. fastepistasis and boost were used to evaluate all pairwise interactions among approximately n = 300,000 single nucleotide polymorphisms (snps) with minor allele frequency (maf) ≥ 0.15, […]

PMCID: 4423967
PMID: 25950439
DOI: 10.1371/journal.pone.0126880

[…] fixed effects and taking residuals from the fitted model []. finally we performed a full genome-wide screen for pairwise interactions, fitting models of form y = μ + v a + v b + v a×v b + ε, using fastepistasis []. after the single marker and epistatic gwa analyses, we selected the top trait-associated additive variants and/or epistatic pairs with p < 10-x in the respective training set […]

PMCID: 4341885
PMID: 25655172
DOI: 10.1186/s12863-015-0174-3

[…] purposes of this study, we excluded 3,521,114 snp pairs with a total count of less than 50 in any row, or less than 5 in any cell of the contingency table. in addition to force, we performed plink (fastepistasis mode) on the top-ranked 500 pairs to compare the results obtained with both methods., to assess the utility of exhaustive search, we constructed a reference dataset of snps previously […]

PMCID: 4012196
PMID: 24817878
DOI: 10.3389/fgene.2014.00106

[…] has been implemented in the epistasis module of plink () to test pair-wise diallelic by diallelic epistasis for both quantitative and binary traits. an extension of the plink epistasis module, fastepistasis, uses an efficient parallel computation algorithm to test pair-wise interactions. fastepistasis is 15 times faster than plink using a single core computer (). proposed an approach […]

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FastEpistasis institution(s)
Vital-IT Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
FastEpistasis funding source(s)
Swiss Institute of Bioinformatics service grant; Swiss National Science Foundation grant #3100AO-116323/1

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