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Epistasis detection is a hot topic in bioinformatics due to its relevance to the detection of specific phenotypic traits and gene-gene interactions. Here, we present a step-by-step protocol to apply Epi-GTBN, a machine learning-based method based on genetic algorithm and Bayesian network to effectively mine the epistasis loci. Epi-GTBN utilizes the advantages of genetic algorithm that can achieve a global search and avoid falling into local optima incorporating it into the Bayesian network to obtain the best structure of the model. In
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