GSR: Editing - Easypop 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 Easypop. Finally, please take note of the GSR simulator privacy policy.
Easypop
EASYPOP is an individual based model intended to simulate datasets under a very broad range of conditions
EASYPOP can simulate haploid, diploid or haplodiploid data. For diploids there is the choice between hermaphrodites or sexuals. For hermaphrodites, the proportion of clonal reproduction and selfing can be chosen, whereas for sexuals, complex breeding structures can be simulated (e.g. monogamy with a given proportion of extra-pair matings). The number of individuals can be selected for each population and dispersal is sex-specific. There are various migration models such as two-dimensional stepping stone or hierarchical island model. In addition there is an isolation-by-distance option which works with the coordinates of the populations on any number of dimensions. There are also several mutation models implemented, which are particularly oriented on the simulation of microsatellite loci. Genotypes are real multilocus, (i.e. there are not independent replicates for each locus). All mutation parameters can be set individually for each locus. EASYPOP is able to handle very large simulations on standard personal computers and is limited only by the memory of the machine. The computer code has been optimized for maximum speed. This allows running very large simulations on personal computers in a reasonable amount of time. In order to fit to analytical xpectations in particular for variances, the functions implemented in EASYPOP are probabilistic and not deterministic. In other words, the simulations rely on the genertation of random numbers.
2.0.1
06-14-2000
06-01-2006
https://www.unil.ch/dee/en/home/menuinst/open-positions-and-public-resources/softwares--dataset/softwares/easypop.html
None

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
    • 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: 11447253], Balloux F, EASYPOP (version 1.7): a computer program for population genetics simulations., J Hered, 05-01-2001, https://www.ncbi.nlm.nih.gov/pubmed/?term=11447253,Primary Citation
      [Pubmed ID: 25799102], Guildea C, Hitchen Y, Duffy R, Dias PJ, Ledger JM, Snow M, Kennington WJ, Introgression threatens the survival of the critically endangered freshwater crayfish Cherax tenuimanus (Decapoda: Parastacidae) in the wild., PLoS One, 03-23-2015, https://www.ncbi.nlm.nih.gov/pubmed/?term=25799102,, Application
      [Pubmed ID: 26080393], Parreira BR, Chikhi L, On some genetic consequences of social structure, mating systems, dispersal, and sampling., Proc Natl Acad Sci U S A, 06-30-2015, https://www.ncbi.nlm.nih.gov/pubmed/?term=26080393,, Application
      [Pubmed ID: 26314287], Momigliano P, Harcourt R, Robbins WD, Stow A, Connectivity in grey reef sharks (Carcharhinus amblyrhynchos) determined using empirical and simulated genetic data., Sci Rep, 08-28-2015, https://www.ncbi.nlm.nih.gov/pubmed/?term=26314287,, Application
      [Pubmed ID: 26649426], Kvistad L, Ingwersen D, Pavlova A, Bull JK, Sunnucks P, Very Low Population Structure in a Highly Mobile and Wide-Ranging Endangered Bird Species., PLoS One, 12-09-2015, https://www.ncbi.nlm.nih.gov/pubmed/?term=26649426,, Application
      [Pubmed ID: 27606008], Gracianne C, Jan PL, Fournet S, Olivier E, Arnaud JF, Porte C, Bardou-Valette S, Denis MC, Petit EJ, Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 2. Separating the relative effects of gene flow and genetic drift., Evol Appl, 07-22-2016, https://www.ncbi.nlm.nih.gov/pubmed/?term=27606008,, Application
      [Pubmed ID: 27814382], Rojas-Hernandez N, Veliz D, Riveros MP, Fuentes JP, Pardo LM, Highly Connected Populations and Temporal Stability in Allelic Frequencies of a Harvested Crab from the Southern Pacific Coast., PLoS One, 11-04-2016, https://www.ncbi.nlm.nih.gov/pubmed/?term=27814382,, Application
      [Pubmed ID: 28235066], Pelletier A, Obbard ME, Harnden M, McConnell S, Howe EJ, Burrows FG, White BN, Kyle CJ, Determining causes of genetic isolation in a large carnivore (Ursus americanus) population to direct contemporary conservation measures., PLoS One, 02-24-2017, https://www.ncbi.nlm.nih.gov/pubmed/?term=28235066,, Application
      [Pubmed ID: 28830924], Kuismin MO, Ahlinder J, Sillanpӓӓ MJ, CONE: Community Oriented Network Estimation Is a Versatile Framework for Inferring Population Structure in Large-Scale Sequencing Data., G3 (Bethesda), 10-05-2017, https://www.ncbi.nlm.nih.gov/pubmed/?term=28830924,, 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).