SeqSIMLA can simulate sequence data in families with multiple affected and unaffected siblings or unrelated case-control under different disease models. Two disease models (the prevalence and population attributable risk models) are provided in SeqSIMLA. Alternatively, a penetrance table can be provided directly to SeqSIMLA. SeqSIMLA can also simulate quantitative traits while accounting for correlations in families.

Recent Update(2015/09/17): Bug fiexed. see more in change log.

New features:

  • Run SeqSIMLA online.
  • Simulate disease and/or quantitative traits
  • Simulate unrelated case-control and/or family data
  • Accept user-specified pedigree structures
  • Simulate correlated quantitative traits considering shared environmental effects in families
  • Accept user-specified penetrance tables for the disease model, which allows for simulating gene-gene interactions
  • Exact simulation for disease status.


  • If you are using the exact option in SeqSIMLA2 for publication, please cite:
    Yao PJ, Chung RH. 2016. SeqSIMLA2_exact: simulate multiple disease sites in large pedigrees with given disease status for diseases with low prevalence. Bioinformatics. 32(4):557-62.
  • If you are using SeqSIMLA2 for publication, please cite:
    hung RH, Tsai WY, Hsieh CH, Hung KY, Hsiung CA, Hauser ER. 2014. SeqSIMLA2: Simulating Correlated Quantitative Traits Accounting for Shared Environmental Effects in User-Specified Pedigree Structure. Genetic Epidemiology. 39(1):20-4.
  • If you are using SeqSIMLA1 for publication, please cite:
    Chung RH, Shih CC. 2013. SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies. BMC Bioinformatics. 14:199