GSR: Editing - SFS_CODE 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 SFS_CODE. Finally, please take note of the GSR simulator privacy policy.
SFS_CODE
SFS_CODE can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects.
SFS_CODE (Selection on Finite Sites under COmplex Demographic Events) performs forward population genetic simulations under a general Wright-Fisher model with arbitrary demographic, selective, and mutational effects.
20100203
02-24-2009
03-26-2012
http://sfscode.sourceforge.net/SFS_CODE/index/index.html

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
      • Sex Chromosomes
      • Mitochondrial DNA
      • Protein Sequence
      • Sequencing Reads
      • Phenotype
    • 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
      • Other
  • Simulation Method
    • Standard Coalescent
    • Exact Coalescent
    • Machine Learning
    • Forward-time
    • Resample Existing Data
    • Phylogenetic
    • Gene dropping
    • 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
      • 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: 18842601], Hernandez RD, A flexible forward simulator for populations subject to selection and demography., Bioinformatics, 12-01-2008, https://www.ncbi.nlm.nih.gov/pubmed/?term=18842601,Primary Citation
      [Pubmed ID: 24273554], Crisci JL, Poh YP, Mahajan S, Jensen JD, The impact of equilibrium assumptions on tests of selection., Front Genet, 01-01-2013, https://www.ncbi.nlm.nih.gov/pubmed/?term=24273554,, Application
      [Pubmed ID: 24360806], He Z, O'Roak BJ, Smith JD, Wang G, Hooker S, Santos-Cortez RL, Li B, Kan M, Krumm N, Nickerson DA, Shendure J, et al., Rare-variant extensions of the transmission disequilibrium test: application to autism exome sequence data., Am J Hum Genet, 01-02-2014, https://www.ncbi.nlm.nih.gov/pubmed/?term=24360806,, Application
      [Pubmed ID: 24415951], Wilson Sayres MA, Lohmueller KE, Nielsen R, Natural selection reduced diversity on human y chromosomes., PLoS Genet, 01-01-2014, https://www.ncbi.nlm.nih.gov/pubmed/?term=24415951,, Application
      [Pubmed ID: 24723422], Simkin AT, Bailey JA, Gao FB, Jensen JD, Inferring the evolutionary history of primate microRNA binding sites: overcoming motif counting biases., Mol Biol Evol, 07-01-2014, https://www.ncbi.nlm.nih.gov/pubmed/?term=24723422,, Application
      [Pubmed ID: 24885734], Sjöstrand AE, Sjödin P, Jakobsson M, Private haplotypes can reveal local adaptation., BMC Genet, 05-22-2014, https://www.ncbi.nlm.nih.gov/pubmed/?term=24885734,, Application
      [Pubmed ID: 25279984], Fu W, Gittelman RM, Bamshad MJ, Akey JM, Characteristics of neutral and deleterious protein-coding variation among individuals and populations., Am J Hum Genet, 10-02-2014, https://www.ncbi.nlm.nih.gov/pubmed/?term=25279984,, Application
      [Pubmed ID: 26681995], Zhang Q, Tyler-Smith C, Long Q, An extended Tajima's D neutrality test incorporating SNP calling and imputation uncertainties., Stat Interface, 10-01-2015, https://www.ncbi.nlm.nih.gov/pubmed/?term=26681995,, Application
      [Pubmed ID: 26897757], Subramanian S, The effects of sample size on population genomic analyses--implications for the tests of neutrality., BMC Genomics, 02-20-2016, https://www.ncbi.nlm.nih.gov/pubmed/?term=26897757,, Application
      [Pubmed ID: 26931140], Lapierre M, Blin C, Lambert A, Achaz G, Rocha EP, The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography., Mol Biol Evol, 07-01-2016, https://www.ncbi.nlm.nih.gov/pubmed/?term=26931140,, Application
      [Pubmed ID: 27498855], Kang L, Zheng HX, Zhang M, Yan S, Li L, Liu L, Liu K, Hu K, Chen F, Ma L, Qin Z, et al., MtDNA analysis reveals enriched pathogenic mutations in Tibetan highlanders., Sci Rep, 08-08-2016, https://www.ncbi.nlm.nih.gov/pubmed/?term=27498855,, 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).