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GPOPSIM specifications

Information


Unique identifier OMICS_22628
Name GPOPSIM
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data A data file including pedigree information, the individuals and their parent identities, and the simulated true genetic value and phenotypic value for each trait and each individual; marker genotype file providing the marker genotypes in phased format; QTL genotype file providing the true QTL genotypes; and several separate parameter files include a marker map file, a true QTL map file.
Operating system Unix/Linux, Windows
Programming languages Fortran
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Xiangdong Ding

Publication for GPOPSIM

GPOPSIM citations

 (4)
library_books

Fast genomic prediction of breeding values using parallel Markov chain Monte Carlo with convergence diagnosis

2018
BMC Bioinformatics
PMCID: 5751823
PMID: 29298666
DOI: 10.1186/s12859-017-2003-3

[…] The simulated data set consisted of 1000 animals in scenario 1 and scenario 2 and 2000 animals in scenario 3, with each presenting a phenotype and genotypes on five chromosomes. The GPOPSIM software package [] was used to generate the simulation data set, including the markers and QTLs based on a mutation-drift equilibrium model in the three scenarios. In scenario 1, the heritabi […]

library_books

Genomic prediction with parallel computing for slaughter traits in Chinese Simmental beef cattle using high density genotypes

2017
PLoS One
PMCID: 5516975
PMID: 28723906
DOI: 10.1371/journal.pone.0179885

[…] We evaluated predictive accuracies and running time of our algorithm in simulation. Here, GPOPSIM software was used to generate simulation dataset including markers and QTLs []. Heritability was set to 0.5, the population included 1000 individuals, each chromosome included 10000 markers an […]

library_books

Bayesian methods for jointly estimating genomic breeding values of one continuous and one threshold trait

2017
PLoS One
PMCID: 5391971
PMID: 28410429
DOI: 10.1371/journal.pone.0175448

[…] To evaluate the proposed method LT-BayesCπ, we carried out a series of simulations using the multiple-trait genomic simulation software GPOPSIM []. For simplicity, we simulated a continuous and a binary threshold trait with different genetic correlation levels between them.Briefly, the simulation started with a base population consist […]

library_books

Joint prediction of multiple quantitative traits using a Bayesian multivariate antedependence model

2015
Heredity
PMCID: 4815501
PMID: 25873147
DOI: 10.1038/hdy.2015.9

[…] A whole-genome simulation program, GPOPSIM (), which is based on the mutation-drift equilibrium model, was used to generate biallelic markers and QTLs. The simulation started with a base population of 100 individuals (50 unrelated male […]

Citations

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GPOPSIM institution(s)
Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; 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, China
GPOPSIM funding source(s)
Supported by the National Natural Science Foundation of China (31200925, 31272418, 31371258), the Program for Changjiang Scholar and Innovation Research Team in University (Grant No. IRT1191), the earmarked fund for China Agriculture Research System (CARS-36), Beijing City Committee of Science and Technology Key Project, and the Ph.D. Programs Foundation (the Doctoral Fund) of Ministry of Education of China (20124404120001).

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