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QMSim specifications

Information


Unique identifier OMICS_15331
Name QMSim
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data A parameter file, in which various parameters for the simulation are specified.
Output data Pedigree information, population structure, phenotypes, true genetic values, crossover positions, LD statistics, linkage map, phased genotypes and allele frequencies and effects.
Output format TXT
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Medium
Version 1.10
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Mehdi Sargolzaei

Publication for QMSim

QMSim citations

 (14)
library_books

Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle

2018
BMC Genomics
PMCID: 5787230
PMID: 29374456
DOI: 10.1186/s12864-018-4453-z

[…] A base population consisted of 500 females and 50 males was simulated using QMSim []. Sixty overlapping generations were generated by mating 50 sires at random to 500 dams. Each dam produced two progeny in each generation. Sire and dam replacement rates were 0.5 and 0.3, resp […]

library_books

Incorporation of causative quantitative trait nucleotides in single step GBLUP

2017
PMCID: 5530494
PMID: 28747171
DOI: 10.1186/s12711-017-0335-0

[…] Using the software QMSim [], we simulated a livestock population under selection for a single quantitative trait that has a heritability of 0.3. A historical population was generated by mutation and drift over 1000 gene […]

call_split

Performance Gains in Genome Wide Association Studies for Longitudinal Traits via Modeling Time varied effects

2017
Sci Rep
PMCID: 5428860
PMID: 28377602
DOI: 10.1038/s41598-017-00638-2
call_split See protocol

[…] ioned. We evaluated statistical power, type-I error rate as well as the accuracy of SNP effect estimated for each GWAS method through 1,000 replication.Population and genomic data were simulated with QMSim software. The simulation started with a base population of 50 males and 50 females in generation −1,000, followed by 1,000 discrete historical generations (generation −1,000 to −1) with the same […]

library_books

Metafounders are related to Fst fixation indices and reduce bias in single step genomic evaluations

2017
PMCID: 5439149
PMID: 28283016
DOI: 10.1186/s12711-017-0309-2

[…] To assess the quality of genomic predictions using one metafounder, we simulated data using QMSim []. The simulation closely followed that in [] to mimic a dairy cattle selection scheme scenario. A historical population undergoing mutation and drift was generated, followed by a recent popula […]

library_books

Systematic genotyping of groups of cows to improve genomic estimated breeding values of selection candidates

2016
PMCID: 5039940
PMID: 27677439
DOI: 10.1186/s12711-016-0250-9

[…] QMSim first simulated a so-called historical population, which consisted of 2000 unrelated animals with a balanced sex ratio. These animals were randomly mated for 2500 generations. To create a suffic […]

library_books

Evaluation of breeding strategies for polledness in dairy cattle using a newly developed simulation framework for quantitative and Mendelian traits

2016
PMCID: 4926303
PMID: 27357942
DOI: 10.1186/s12711-016-0228-7

[…] and stochastic simulation techniques require genetic (co)variance components for both traits. Regarding the situation with polledness, only assumptions can be made since results are not available yet.QMSim [] is a powerful whole-genome stochastic simulation program that was designed to simulate a wide range of genetic and genomic architectures and population structures, particularly in livestock. […]

Citations

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QMSim institution(s)
Department of Animal and Poultry Science, University of Guelph, Guelph, ON, Canada
QMSim funding source(s)
Supported by L’Alliance Boviteq Inc. (SEMEX Alliance, Canada); Natural Sciences and Engineering Research Council of Canada (Collaborative Research and Development grant); Ontario Centre for Agriculture Genomics (Challenge Fund).

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