title: GPOPSIM: a simulation tool for whole-genome genetic data.
abstract: 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.
authors: Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China. zhezhang@scau.edu.cn.
authors: Zhe
authors: Z
authors: Zhang
authors: Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. lixiujin996@gmail.com.
authors: Xiujin
authors: X
authors: Li
authors: Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. xding@cau.edu.cn.
authors: Xiangdong
authors: X
authors: Ding
authors: Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China. jqli@scau.edu.cn.
authors: Jiaqi
authors: J
authors: Li
authors: Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. qzhang@cau.edu.cn.
authors: Qin
authors: Q
authors: Zhang
mesh_terms: D000818:Animals; D003198:Computer Simulation; D005828:Genetics, Population / Q000379:methods*; D055106:Genome-Wide Association Study; D008957:Models, Genetic; D012984:Software
references: J Dairy Sci. 2011 Jul;94(7):3642-50
references: 21700054
references: PLoS One. 2010;5(9). pii: e12648. doi: 10.1371/journal.pone.0012648
references: 20844593
references: Heredity (Edinb). 2013 Mar;110(3):213-9
references: 23149458
references: BMC Bioinformatics. 2013;14:34
references: 23363272
references: Genetics. 1964 Apr;49:725-38
references: 14156929
references: Genetics. 2001 Apr;157(4):1819-29
references: 11290733
references: Theor Popul Biol. 1971 Jun;2(2):125-41
references: 5170716
references: Bioinformatics. 2005 Jan 15;21(2):263-5
references: 15297300
references: Nature. 2007 Jun 7;447(7145):661-78
references: 17554300
references: Genetics. 2008 Jan;178(1):553-61
references: 18202394
references: PLoS One. 2008;3(10):e3395
references: 18852893
references: Curr Opin Genet Dev. 2008 Jun;18(3):257-63
references: 18682292
references: PLoS One. 2009;4(4):e5350
references: 19390634
references: Genetics. 2010 Jun;185(2):623-31
references: 20308278
references: Anim Genet. 2010 Aug;41(4):346-56
references: 20055813
references: Genetics. 2010 Jul;185(3):1021-31
references: 20407128
references: Genet Sel Evol. 2011;43:26
references: 21729282