GSR: Editing - MetaPopGen 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 MetaPopGen. Finally, please take note of the GSR simulator privacy policy.
MetaPopGen
Simulates genetics in large size metapopulations
MetaPopGen is a population genetics simulator. Features included in the model are age-structure, monoecious and dioecious (or separate sexes) life-cycles, mutation, dispersal and selection. All demographic parameters can be genotype-, sex-, age-, deme- and time-dependent. MetaPopGen is therefore indicated to study large populations and very complex demographic scenarios.
2.0.0
10-10-2014
10-19-2020
https://github.com/MarcoAndrello/MetaPopGen
marco.andrello@gmail.com

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

      Claudio S. Quilodrán Kristen Ruegg Ashley T. Sendell‐Price Eric C. Anderson Tim Coulson Sonya M. Clegg, The multiple population genetic and demographic routes to islands of genomic divergence, Methods in Ecology and Evolution, 11-07-2019, https://doi.org/10.1111/2041-210X.13324,, Application
      William Handal Claire Szostek Natalie Hold Marco Andrello Eric Thiébaut Ewan Harney Gwendoline Lefebvre Elodie Borcier Aurélie Jolivet Amandine Nicolle Aurélien Boyé Eric Foucher Pierre Boudry Grégory Charrier, New insights on the population genetic structure of the great scallop (Pecten maximus) in the English Channel, coupling microsatellite data and demogenetic simulations, Aquatic Conservation: marine and freshwater ecosystems, 09-04-2020, https://doi.org/10.1002/aqc.3316,, Application
      [Pubmed ID: 25585533], Andrello M, Manel S, MetaPopGen: an r package to simulate population genetics in large size metapopulations., Mol Ecol Resour, 01-13-2015, https://www.ncbi.nlm.nih.gov/pubmed/?term=25585533,Primary Citation
      [Pubmed ID: 27736016], Parobek CM, Archer FI, DePrenger-Levin ME, Hoban SM, Liggins L, Strand AE, skelesim: an extensible, general framework for population genetic simulation in R., Mol Ecol Resour, 01-01-2017, https://www.ncbi.nlm.nih.gov/pubmed/?term=27736016,, Application
      [Pubmed ID: 31769930], Landguth EL, Forester BR, Eckert AJ, Shirk AJ, Menon M, Whipple A, Day CC, Cushman SA, Modelling multilocus selection in an individual-based, spatially-explicit landscape genetics framework., Mol Ecol Resour, 03-01-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=31769930,, Application
      [Pubmed ID: 32034102], Smith AL, Hodkinson TR, Villellas J, Catford JA, Csergő AM, Blomberg SP, Crone EE, Ehrlén J, Garcia MB, Laine AL, et al., Global gene flow releases invasive plants from environmental constraints on genetic diversity., Proc Natl Acad Sci U S A, 02-25-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=32034102,, Application
      [Pubmed ID: 33030758], Andrello M, Noirot C, Débarre F, Manel S, MetaPopGen 2.0: A multilocus genetic simulator to model populations of large size., Mol Ecol Resour, 02-01-2021, https://www.ncbi.nlm.nih.gov/pubmed/?term=33030758,Primary Citation
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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).