GSR: Editing - QMSim Simulator

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QMSim
QTL and Marker Simulator
Linkage disequilibrium (LD) and linkage analyses have been used extensively to identify quantitative trait loci (QTL) in human and livestock. Owing to the recent developments in genotyping technologies, dense marker maps are now available for several livestock species. Even though genotyping costs have substantially declined, large scale genome-wide association studies are still costly. For this reason many studies in livestock suffer from small sample size or from low density of markers. However, simulation is a highly valuable tool for assessing and validating new proposed methods for association studies at very low cost. During the last few decades, simulation has played a major role in answering a wide variety of questions in genomics. Several software have been developed for simulating genomes especially in human research. However most of the developed software tools do not provide functionality required for many of the applications in livestock. QMSim was developed to simulate large scale genomic data in livestock populations. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex.
1.1.0
02-09-2009
07-12-2013
http://www.aps.uoguelph.ca/~msargol/qmsim/

Attribute Tree Control

Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator.
Every sub-attribute is selected
Not all sub-attributes are selected
  • Target
    • Type of Simulated Data
      • Genotype at Genetic Markers
      • Diploid DNA Sequence
      • Haploid DNA Sequence
      • RNA
      • Gene Expression
      • Sex Chromosomes
      • Mitochondrial DNA
      • Protein Sequence
      • Sequencing Reads
      • Phenotype
      • Single-Cell Sequencing
      • Bulk Sequencing
      • Proteomics
      • Chromatin Conformation
    • Variations
      • Biallelic Marker
      • Multiallelic Marker
      • Single Nucleotide Variation
      • Amino acid variation
      • Microsatellite
      • Insertion and Deletion
      • CNV
      • Inversion and Rearrangement
      • Alternative Splicing
      • Missing Genotypes
      • Genotype or Sequencing Error
      • Ionization
      • Other
  • Simulation Method
    • Standard Coalescent
    • Exact Coalescent
    • Machine Learning
    • Forward-time
    • Resample Existing Data
    • Phylogenetic
    • Gene dropping
    • Neural network
    • Other
  • Input
    • Data Type
      • Allele Frequencies
      • Empirical
      • Ancestral Sequence
      • Saved simulation
      • Reference genome
      • Other
    • File format
      • Arlequin
      • CREATE
      • Fstat
      • GDA
      • Genepop
      • MIGRATE
      • MS
      • SAM or BAM
      • NEXUS
      • Phylip
      • STRUCTURE
      • XML
      • Tree Sequence
      • Program Specific
      • Other
  • Output
    • Data Type
      • Genotype or Sequence
      • Phenotypic Trait
      • Individual Relationship
      • Phylogenetic Tree
      • Demographic
      • Mutation
      • Methylation
      • Gene Expression
      • Protein Expression
      • Linkage Disequilibrium
      • Diversity Measures
      • Fitness
      • Sequencing Reads
        • Illumina
        • Roche 454
        • SOLiD
        • IonTorrent
        • PacBio
        • Nanopore
        • Other
      • Other
    • File Format
      • Arlequin
      • Fasta or Fastq
      • Fstat
      • Genepop
      • Linkage
      • MIGRATE
      • MS
      • PED
      • Phylip
      • NEXUS
      • STRUCTURE
      • VCF
      • SAM or BAM
      • Tree Sequence
      • Program Specific
      • Other
    • Sample Type
      • Random or Independent
      • Sibpairs, Trios and Nuclear Families
      • Extended or Complete Pedigrees
      • Case-control
      • Longitudinal
      • Other
  • Phenotype
    • Trait Type
      • Binary or Qualitative
      • Quantitative
      • Multiple
    • Determinants
      • Single Genetic Marker
      • Multiple Genetic Markers
      • Sex-linked
      • Gene-Gene Interaction
      • Environmental Factors
      • Gene-Environment Interaction
  • Evolutionary Features
    • Demographic
      • Population Size Changes
        • Constant Size
        • Exponential Growth or Decline
        • Logistic Growth
        • Bottleneck
        • Carrying Capacity
        • User Defined
      • Gene Flow
        • Stepping Stone Models
        • Island Models
        • Continent-Island Models
        • Sex or Age-Specific Migration Rates
        • Influenced by Environmental Factors
        • Admixed Population
        • User-defined Matrix
        • Other
      • Spatiality
        • Discrete Models
        • Continuous Models
        • Landscape Factors
    • Life Cycle
      • Discrete Generation Model
      • Age structured
      • Overlapping Generation
      • User-Defined transition matrices
    • Mating System
      • Random Mating
      • Monogamous
      • Polygamous
      • Haplodiploid
      • Selfing
      • Age- or Stage-Specific
      • Assortative or Disassortative
      • Other
    • Fecundity
      • Constant Number
      • Randomly Distributed
      • Individually Determined
      • Influenced by Environment
      • Other
    • Natural Selection
      • Determinant
        • Single-locus
        • Multi-locus
        • Codon-based
        • Fitness of Offspring
        • Phenotypic Trait
        • Environmental Factors
      • Models
        • Directional Selection
        • Balancing Selection
        • Multi-locus models
        • Epistasis
        • Random Fitness Effects
        • Disruptive
        • Phenotype Threshold
        • Frequency-Dependent
        • Other
    • Recombination
      • Uniform
      • Varying Recombination Rates
      • Gene Conversion Allowed
    • Mutation Models
      • Two-allele Mutation Model
      • Markov DNA Evolution Models
      • k-Allele Model
      • Infinite-allele Model
      • Infinite-sites Model
      • Stepwise Mutation Model
      • Codon and Amino Acid Models
      • Indels and Others
      • Heterogeneity among Sites
      • Others
    • Events Allowed
      • Population Merge and Split
      • Varying Demographic Features
      • Population Events
      • Varying Genetic Features
      • Change of Mating Systems
      • Other
    • Other
      • Phenogenetic
      • Polygenic background
  • Interface
    • Command-line
    • Graphical User Interface
    • Integrated Development Environment
    • Script-based
    • Web-based
  • Development
    • Tested Platforms
      • Windows
      • Mac OS X
      • Linux and Unix
      • Solaris
      • Others
    • Language
      • C or C++
      • Java
      • R
      • Python
      • Perl
      • Visual Basic
      • Other
    • License
      • GNU Public License
      • BSD
      • Creative Commons
      • MIT
      • Other
  • GSR Certification
    • Accessibility
    • Documentation
    • Application
    • Support

Summary of Proposed Changes

Step 2: Review list of proposed attribute addition(s) and subtraction(s).

To Add

    To Remove

      Can't Find the Attribute You Are Looking For?

      If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the Additional Comment box of the Submit tab.

      You may add citations by pmid, add citations by direct entry, remove citations (using the recycling bin icon), and edit citations (using the rarely seen edit icon) that were originally entered by direct entry.

      Summary of Proposed Changes

      To Add

      To Remove

      Current Citations/Applications

      [Pubmed ID: 19176551], Sargolzaei M, Schenkel FS, QMSim: a large-scale genome simulator for livestock., Bioinformatics, 03-01-2009, https://www.ncbi.nlm.nih.gov/pubmed/?term=19176551,Primary Citation
      [Pubmed ID: 32554752], González-Diéguez D, Tusell L, Bouquet A, Legarra A, Vitezica ZG, Purebred and Crossbred Genomic Evaluation and Mate Allocation Strategies To Exploit Dominance in Pig Crossbreeding Schemes., G3 (Bethesda), 08-05-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=32554752,, Application
      [Pubmed ID: 32727349], Jibrila I, Ten Napel J, Vandenplas J, Veerkamp RF, Calus MPL, Investigating the impact of preselection on subsequent single-step genomic BLUP evaluation of preselected animals., Genet Sel Evol, 07-29-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=32727349,, Application
      [Pubmed ID: 32751408], Manca E, Cesarani A, Gaspa G, Sorbolini S, Macciotta NPP, Dimauro C, Use of the Multivariate Discriminant Analysis for Genome-Wide Association Studies in Cattle., Animals (Basel), 07-29-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=32751408,, Application
      [Pubmed ID: 32760564], Chen SY, Li C, Luo Z, Li X, Gan J, Jia X, Lai SJ, Wang W, Genotyping-free parentage assignment using RAD-seq reads., Ecol Evol, 06-30-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=32760564,, Application
      [Pubmed ID: 32819072], Nwogwugwu CP, Kim Y, Choi H, Lee JH, Lee SH, Assessment of genomic prediction accuracy using different selection and evaluation approaches in a simulated Korean beef cattle population., Asian-Australas J Anim Sci, 12-01-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=32819072,, Application
      [Pubmed ID: 32819970], Esfandyari H, Fè D, Tessema BB, Janss LL, Jensen J, Effects of Different Strategies for Exploiting Genomic Selection in Perennial Ryegrass Breeding Programs., G3 (Bethesda), 10-05-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=32819970,, Application
      [Pubmed ID: 32985749], Bermann M, Legarra A, Hollifield MK, Masuda Y, Lourenco D, Misztal I, Validation of single-step GBLUP genomic predictions from threshold models using the linear regression method: An application in chicken mortality., J Anim Breed Genet, 01-01-2021, https://www.ncbi.nlm.nih.gov/pubmed/?term=32985749,, Application
      [Pubmed ID: 33158416], Wientjes YCJ, Bijma P, Calus MPL, Optimizing genomic reference populations to improve crossbred performance., Genet Sel Evol, 11-06-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=33158416,, Application
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      Please inform the GSR team here if you would like to see an attribute added to the attribute tree (or any other changes to the simulator description system as it exists).