GSR: Editing - CDPOP 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 CDPOP. Finally, please take note of the GSR simulator privacy policy.
CDPOP
CDPOP is a landscape genetics tool for simulating the emergence of spatial genetic structure in populations resulting from specified landscape processes governing organism movement behavior.
CDPOP (Cost Distance POPulations) is an individual-based simulator of gene flow in complex landscapes to explain observed population responses and provide a foundation for landscape genetics. It models genetic exchange among spatially located individuals as a function of individual-based movement through mating and dispersal, incorporating population dynamics and the all factors that affect the frequency of an allele in a population (mutation, gene flow, genetic drift, and selection). User’s initially specify individual locations, environmental conditions governing gene flow, spatially-explicit fitness landscapes governing selection, and various genic configurations, and CDPOP models divergence through time as function of individual-based movement, breeding and dispersal as functions of the given landscape surfaces.
1.0 or later
Jan. 1, 2010
Aug. 10, 2016
https://github.com/ComputationalEcologyLab/CDPOP

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

      Shirk AJ, Landguth EL, Cushman SA, A comparison of individual-based genetic distance metrics for landscape genetics., Mol Ecol Resour, 11-01-2017, , Application
      Stucki S, Orozco-terWengel P, Forester BR, Duruz S, Colli L, Masembe C, Negrini R, Landguth E, Jones MR, Bruford MW, Taberlet P, et al., High performance computation of landscape genomic models including local indicators of spatial association., Mol Ecol Resour, 09-01-2017, , Application
      Landguth EL, Schwartz M., Evaluating sample allocation and effort in detecting population differentiation for discrete and continuously distributed individuals, Conservation Genetics, 08-01-2014, , Application
      Cooke GM, Landguth EL, Beheregaray LB, Riverscape genetics identifies replicated ecological divergence across an Amazonian ecotone., Evolution, 07-01-2014, , Application
      Landguth EL, Johnson NA, Cushman SA, Clusters of incompatible genotypes evolve with limited dispersal., Front Genet, 01-01-2015, , Application
      Cushman SA, Landguth EL, Spatially Heterogeneous Environmental Selection Strengthens Evolution of Reproductively Isolated Populations in a Dobzhansky-Muller System of Hybrid Incompatibility., Front Genet, 01-01-2016, , Application
      Forester BR, Jones MR, Joost S, Landguth EL, Lasky JR, Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes., Mol Ecol, 01-01-2016, , Application
      Smith AL, Landguth EL, Bull CM, Banks SC, Gardner MG, Driscoll DA, Dispersal responses override density effects on genetic diversity during post-disturbance succession., Proc Biol Sci, 03-30-2016, , Application
      Zeller KA, Creech TG, Millette KL, Crowhurst RS, Long RA, Wagner HH, Balkenhol N, Landguth EL, Using simulations to evaluate Mantel-based methods for assessing landscape resistance to gene flow., Ecol Evol, 06-01-2016, , Application
      Creech TG, Epps CW, Landguth EL, Wehausen JD, Crowhurst RS, Holton B, Monello RJ, Simulating the spread of selection-driven genotypes using landscape resistance models for desert bighorn sheep., PLoS One, 01-01-2017, , Application
      Shirk AJ, Landguth EL, Cushman SA, A comparison of regression methods for model selection in individual-based landscape genetic analysis., Mol Ecol Resour, 08-10-2017, , Application
      [Pubmed ID: 20618896], Cushman SA, Landguth EL, Spurious correlations and inference in landscape genetics., Mol Ecol, 09-01-2010, https://www.ncbi.nlm.nih.gov/pubmed/?term=20618896,, Application
      [Pubmed ID: 20819159], Landguth EL, Cushman SA, Schwartz MK, McKelvey KS, Murphy M, Luikart G, Quantifying the lag time to detect barriers in landscape genetics., Mol Ecol, 10-01-2010, https://www.ncbi.nlm.nih.gov/pubmed/?term=20819159,, Application
      [Pubmed ID: 21565001], Landguth EL, Cushman SA, cdpop: A spatially explicit cost distance population genetics program., Mol Ecol Resour, 01-01-2010, https://www.ncbi.nlm.nih.gov/pubmed/?term=21565001,Primary Citation
      [Pubmed ID: 21565096], Landguth EL, Cushman SA, Murphy MA, Luikart G, Relationships between migration rates and landscape resistance assessed using individual-based simulations., Mol Ecol Resour, 09-01-2010, https://www.ncbi.nlm.nih.gov/pubmed/?term=21565096,, Application
      [Pubmed ID: 21951716], Landguth EL, Cushman SA, Johnson NA, Simulating natural selection in landscape genetics., Mol Ecol Resour, 03-01-2012, https://www.ncbi.nlm.nih.gov/pubmed/?term=21951716,, Application
      [Pubmed ID: 22551194], Blair C, Weigel DE, Balazik M, Keeley AT, Walker FM, Landguth E, Cushman S, Murphy M, Waits L, Balkenhol N, A simulation-based evaluation of methods for inferring linear barriers to gene flow., Mol Ecol Resour, 09-01-2012, https://www.ncbi.nlm.nih.gov/pubmed/?term=22551194,, Application
      [Pubmed ID: 24299400], Jones MR, Forester BR, Teufel AI, Adams RV, Anstett DN, Goodrich BA, Landguth EL, Joost S, Manel S, Integrating landscape genomics and spatially explicit approaches to detect loci under selection in clinal populations., Evolution, 12-01-2013, https://www.ncbi.nlm.nih.gov/pubmed/?term=24299400,, Application
      [Pubmed ID: 24641091], Cooke GM, Landguth EL, Beheregaray LB, Riverscape genetics identifies replicated ecological divergence across an Amazonian ecotone., Evolution, 07-01-2014, https://www.ncbi.nlm.nih.gov/pubmed/?term=24641091,, Application
      [Pubmed ID: 25653668], Beheregaray LB, Cooke GM, Chao NL, Landguth EL, Ecological speciation in the tropics: insights from comparative genetic studies in Amazonia., Front Genet, 01-01-2014, https://www.ncbi.nlm.nih.gov/pubmed/?term=25653668,, Application
      [Pubmed ID: 25954302], Landguth EL, Johnson NA, Cushman SA, Clusters of incompatible genotypes evolve with limited dispersal., Front Genet, 01-01-2015, https://www.ncbi.nlm.nih.gov/pubmed/?term=25954302,, Application
      [Pubmed ID: 26576498], Forester BR, Jones MR, Joost S, Landguth EL, Lasky JR, Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes., Mol Ecol, 01-01-2016, https://www.ncbi.nlm.nih.gov/pubmed/?term=26576498,, Application
      [Pubmed ID: 27009225], Smith AL, Landguth EL, Bull CM, Banks SC, Gardner MG, Driscoll DA, Dispersal responses override density effects on genetic diversity during post-disturbance succession., Proc Biol Sci, 03-30-2016, https://www.ncbi.nlm.nih.gov/pubmed/?term=27009225,, Application
      [Pubmed ID: 27516868], Zeller KA, Creech TG, Millette KL, Crowhurst RS, Long RA, Wagner HH, Balkenhol N, Landguth EL, Using simulations to evaluate Mantel-based methods for assessing landscape resistance to gene flow., Ecol Evol, 06-01-2016, https://www.ncbi.nlm.nih.gov/pubmed/?term=27516868,, Application
      [Pubmed ID: 27801969], Stucki S, Orozco-terWengel P, Forester BR, Duruz S, Colli L, Masembe C, Negrini R, Landguth E, Jones MR, Bruford MW, Taberlet P, et al., High performance computation of landscape genomic models including local indicators of spatial association., Mol Ecol Resour, 09-01-2017, https://www.ncbi.nlm.nih.gov/pubmed/?term=27801969,, Application
      [Pubmed ID: 27933091], Cushman SA, Landguth EL, Spatially Heterogeneous Environmental Selection Strengthens Evolution of Reproductively Isolated Populations in a Dobzhansky-Muller System of Hybrid Incompatibility., Front Genet, 01-01-2016, https://www.ncbi.nlm.nih.gov/pubmed/?term=27933091,, Application
      [Pubmed ID: 28449317], Shirk AJ, Landguth EL, Cushman SA, A comparison of individual-based genetic distance metrics for landscape genetics., Mol Ecol Resour, 11-01-2017, https://www.ncbi.nlm.nih.gov/pubmed/?term=28449317,, Application
      [Pubmed ID: 28464013], Creech TG, Epps CW, Landguth EL, Wehausen JD, Crowhurst RS, Holton B, Monello RJ, Simulating the spread of selection-driven genotypes using landscape resistance models for desert bighorn sheep., PLoS One, 01-01-2017, https://www.ncbi.nlm.nih.gov/pubmed/?term=28464013,, Application
      [Pubmed ID: 28796434], Shirk AJ, Landguth EL, Cushman SA, A comparison of regression methods for model selection in individual-based landscape genetic analysis., Mol Ecol Resour, 08-10-2017, https://www.ncbi.nlm.nih.gov/pubmed/?term=28796434,, 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).