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Background  Population-wide genotypic and phenotypic data is frequently used to predict the disease risk or genetic/phenotypic values, or to localize genetic variations responsible for complex traits. GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can simulate multiple genetically correlated traits with desired genetic parameters and underlying genetic architectures.    Results  The model implemented in GPOPSIM is presented, and the code has been made freely available to the community. Data simulated by GPOPSIM is a good mimic to the real data in terms of genome structure and trait underlying genetic architecture.    Conclusions  GPOPSIM would be a useful tool for the methodological and theoretical studies in the population and quantitative genetics and breeding.    Electronic supplementary material  The online version of this article (doi:10.1186/s12863-015-0173-4) contains supplementary material, which is available to authorized users.

GPOPSIM: a simulation tool for whole-genome genetic data