GSR: Editing - FREGENE Simulator

You may request changes to this simulator by navigating to the Basic, Details, and Citations/Applications tabs. When you are finished, open the Submit tab. To return back to the simulator view, click FREGENE. Finally, please take note of the GSR simulator privacy policy.
FREGENE
FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations.
FREGENE works forwards-in-time which allows a wide range of demographic and selection scenarios to be implemented. Many such models are already incorporated into FREGENE, and since it is open source users can modify or extend these. Coalescent methods have difficulty incorporating large amounts of gene conversion or crossover (Hoggart et al. 2007), whereas these pose no particular problem for FREGENE. FREGENE offers a flexible model for recombination hotspots, and can readily simulate regions up to tens of Mb on a standard desktop computer. The principle limitation of forward-in-time algorithms is computational, since the entire population must be tracked through time, not only the chromosomes that are ancestral to the observed sample. FREGENE implements many features to enhance computational efficiency, and includes a rescaling option that greatly reduces computation time at the cost of some approximation.
01-01-2007
08-01-2008
http://www.ebi.ac.uk/projects/BARGEN

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: 18778480], Chadeau-Hyam M, Hoggart CJ, O'Reilly PF, Whittaker JC, De Iorio M, Balding DJ, Fregene: simulation of realistic sequence-level data in populations and ascertained samples., BMC Bioinformatics, 09-08-2008, https://www.ncbi.nlm.nih.gov/pubmed/?term=18778480,Primary Citation
      [Pubmed ID: 20140238], Enard D, Depaulis F, Roest Crollius H, Human and non-human primate genomes share hotspots of positive selection., PLoS Genet, 02-05-2010, https://www.ncbi.nlm.nih.gov/pubmed/?term=20140238,, Application
      [Pubmed ID: 20877324], Powell JE, Visscher PM, Goddard ME, Reconciling the analysis of IBD and IBS in complex trait studies., Nat Rev Genet, 11-01-2010, https://www.ncbi.nlm.nih.gov/pubmed/?term=20877324,, Application
      [Pubmed ID: 21104890], Ayers KL, Cordell HJ, SNP selection in genome-wide and candidate gene studies via penalized logistic regression., Genet Epidemiol, 12-01-2010, https://www.ncbi.nlm.nih.gov/pubmed/?term=21104890,, Application
      [Pubmed ID: 21705750], Keller MC, Visscher PM, Goddard ME, Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data., Genetics, 09-01-2011, https://www.ncbi.nlm.nih.gov/pubmed/?term=21705750,, Application
      [Pubmed ID: 21929786], Cule E, Vineis P, De Iorio M, Significance testing in ridge regression for genetic data., BMC Bioinformatics, 09-19-2011, https://www.ncbi.nlm.nih.gov/pubmed/?term=21929786,, Application
      [Pubmed ID: 21943305], Howrigan DP, Simonson MA, Keller MC, Detecting autozygosity through runs of homozygosity: a comparison of three autozygosity detection algorithms., BMC Genomics, 09-23-2011, https://www.ncbi.nlm.nih.gov/pubmed/?term=21943305,, Application
      [Pubmed ID: 22125225], Lipman PJ, Yip WK, AlChawa T, Ludwig KU, Mangold E, Lange C, On the analysis of sequence data: testing for disease susceptibility loci using patterns of linkage disequilibrium., Genet Epidemiol, 12-01-2011, https://www.ncbi.nlm.nih.gov/pubmed/?term=22125225,, Application
      [Pubmed ID: 22216125], Bouaziz M, Ambroise C, Guedj M, Accounting for population stratification in practice: a comparison of the main strategies dedicated to genome-wide association studies., PLoS One, 01-01-2011, https://www.ncbi.nlm.nih.gov/pubmed/?term=22216125,, Application
      [Pubmed ID: 23077494], Bouaziz M, Paccard C, Guedj M, Ambroise C, SHIPS: Spectral Hierarchical clustering for the Inference of Population Structure in genetic studies., PLoS One, 01-01-2012, https://www.ncbi.nlm.nih.gov/pubmed/?term=23077494,, Application
      [Pubmed ID: 23893343], Cule E, De Iorio M, Ridge regression in prediction problems: automatic choice of the ridge parameter., Genet Epidemiol, 11-01-2013, https://www.ncbi.nlm.nih.gov/pubmed/?term=23893343,, 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).