GSR: Editing - Nemo 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 Nemo. Finally, please take note of the GSR simulator privacy policy.
Nemo
A forward-time, individual-based, genetically explicit, and stochastic simulation program designed to study the evolution of genetic markers, life history traits, and phenotypic traits in a flexible (meta-)population framework.
Nemo implements many different life cycles and evolvable traits with a large variety of genetic architectures. Species interaction between a parasite and its host can also be modeled (i.e., Cytoplasmic-Incompatibility inducing endosymbiont: Wolbachia). All this is framed within a flexible metapopulation model that allows for patch-specific carrying capacities, dispersal rates (dispersal matrices), stochastic extinction/harvesting rates, and demographic stochasticity. Populations can be dynamically modified during a simulation, allowing for population bottlenecks, patch fusion/fission, population expansion, etc. Spatially heterogeneous selection on quantitative traits can also be modeled. Nemo's interface is a simple text file containing the simulation parameters. Large batches of simulations can be run from a single parameter file with multiple parameter values. Many complex evolutionary and demographic scenarios can be modeled easily by providing temporally varying parameter values.
None
2.3.51
05-02-2006
09-27-2018
http://nemo2.sourceforge.net/

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
    • 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
      • NEXUS
      • Phylip
      • STRUCTURE
      • XML
      • Tree Sequence
      • Program Specific
      • Other
  • Output
    • Data Type
      • Genotype or Sequence
      • Phenotypic Trait
      • Individual Relationship
      • Demographic
      • Mutation
      • 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
      • 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

      Gompert Z, and Buerkle CA, What, if anything, are hybrids: enduring truths and challenges associated with population structure and gene flow, Evolutionary Applications, , https://doi.org/10.1111/eva.12380,, Application
      Yeaman S, Gerstein AC, Hodgins KA, and Whitlock MC , Quantifying how constraints limit the diversity of viable routes to adaptation, PLOS Genetics, , https://doi.org/10.1371/journal.pgen.1007717,, Application
      Schmid M, Dallo R, Guillaume F, Species' Range Dynamics Affect the Evolution of Spatial Variation in Plasticity under Environmental Change., Am Nat, 06-01-2019, https://www.ncbi.nlm.nih.gov/pubmed/?term=31094605,, Application
      Chebib J, and Guillaume F, Pleiotropy or linkage? Their relative contributions to the genetic correlation of quantitative traits and detection by multi-trait GWA studies, bioRxiv, , http://biorxiv.org/content/early/2019/11/25/656413.abstract,, Application
      Schmidt TL, Filipovic I, Hoffmann AA, and Rasic G, Fine-scale landscape genomics helps explain the slow spatial spread of Wolbachia through the Aedes aegypti population in Cairns, Australia, Heredity, , https://doi.org/10.1038/s41437-017-0039-9,, Application
      Gilbert KJ, and Whitlock MC, The genetics of adaptation to discrete heterogeneous environments: frequent mutation or large-effect alleles can allow range expansion, Journal of Evolutionary Biology, , https://doi.org/10.1111/jeb.13029,, Application
      Gilbert KJ, Sharp NP, Angert AL, Conte GL, Draghi JA, Guillaume F, Hargreaves AL, Matthey-Doret R, Whitlock MC, Local Adaptation Interacts with Expansion Load during Range Expansion: Maladaptation Reduces Expansion Load., Am Nat, 04-01-2017, https://www.ncbi.nlm.nih.gov/pubmed/?term=28350500,, Application
      Cotto O, Wessely J, Georges D, Klonner G, Schmid M, Dullinger S, Thuiller W, and Guillaume F, A dynamic eco-evolutionary model predicts slow response of alpine plants to climate warming, Nature Communications, , https://doi.org/10.1038/ncomms15399,, Application
      [Pubmed ID: 16510793], Guillaume F, Perrin N, Joint evolution of dispersal and inbreeding load., Genetics, 05-01-2006, https://www.ncbi.nlm.nih.gov/pubmed/?term=16510793,, Application
      [Pubmed ID: 16882649], Guillaume F, Rougemont J, Nemo: an evolutionary and population genetics programming framework., Bioinformatics, 10-15-2006, https://www.ncbi.nlm.nih.gov/pubmed/?term=16882649,Primary Citation
      [Pubmed ID: 17711463], Guillaume F, Whitlock MC, Effects of migration on the genetic covariance matrix., Evolution, 10-01-2007, https://www.ncbi.nlm.nih.gov/pubmed/?term=17711463,, Application
      [Pubmed ID: 18460188], Reuter M, Lehmann L, Guillaume F, The spread of incompatibility-inducing parasites in sub-divided host populations., BMC Evol Biol, 05-06-2008, https://www.ncbi.nlm.nih.gov/pubmed/?term=18460188,, Application
      [Pubmed ID: 18847439], Jaquiéry J, Guillaume F, Perrin N, Predicting the deleterious effects of mutation load in fragmented populations., Conserv Biol, 02-01-2009, https://www.ncbi.nlm.nih.gov/pubmed/?term=18847439,, Application
      [Pubmed ID: 19243259], Guillaume F, Perrin N, Inbreeding load, bet hedging, and the evolution of sex-biased dispersal., Am Nat, 04-01-2009, https://www.ncbi.nlm.nih.gov/pubmed/?term=19243259,, Application
      [Pubmed ID: 19619220], Yeaman S, Guillaume F, Predicting adaptation under migration load: the role of genetic skew., Evolution, 11-01-2009, https://www.ncbi.nlm.nih.gov/pubmed/?term=19619220,, Application
      [Pubmed ID: 19687138], Whitlock MC, Guillaume F, Testing for spatially divergent selection: comparing QST to FST., Genetics, 11-01-2009, https://www.ncbi.nlm.nih.gov/pubmed/?term=19687138,, Application
      [Pubmed ID: 21644959], Guillaume F, Migration-induced phenotypic divergence: the migration-selection balance of correlated traits., Evolution, 06-01-2011, https://www.ncbi.nlm.nih.gov/pubmed/?term=21644959,, Application
      [Pubmed ID: 21729046], Yeaman S, Whitlock MC, The genetic architecture of adaptation under migration-selection balance., Evolution, 07-01-2011, https://www.ncbi.nlm.nih.gov/pubmed/?term=21729046,, Application
      [Pubmed ID: 22026559], Lin JE, Hilborn R, Quinn TP, Hauser L, Self-sustaining populations, population sinks or aggregates of strays: chum (Oncorhynchus keta) and Chinook salmon (Oncorhynchus tshawytscha) in the Wood River system, Alaska., Mol Ecol, 12-01-2011, https://www.ncbi.nlm.nih.gov/pubmed/?term=22026559,, Application
      [Pubmed ID: 22982578], Guillaume F, Otto SP, Gene functional trade-offs and the evolution of pleiotropy., Genetics, 12-01-2012, https://www.ncbi.nlm.nih.gov/pubmed/?term=22982578,, Application
      [Pubmed ID: 23025607], Zhang H, Guillaume F, Engelstädter J, The dynamics of mitochondrial mutations causing male infertility in spatially structured populations., Evolution, 10-01-2012, https://www.ncbi.nlm.nih.gov/pubmed/?term=23025607,, Application
      [Pubmed ID: 23610436], Yeaman S, Genomic rearrangements and the evolution of clusters of locally adaptive loci., Proc Natl Acad Sci U S A, 05-07-2013, https://www.ncbi.nlm.nih.gov/pubmed/?term=23610436,, Application
      [Pubmed ID: 28350500], Gilbert KJ, Sharp NP, Angert AL, Conte GL, Draghi JA, Guillaume F, Hargreaves AL, Matthey-Doret R, Whitlock MC, Local Adaptation Interacts with Expansion Load during Range Expansion: Maladaptation Reduces Expansion Load., Am Nat, 04-01-2017, https://www.ncbi.nlm.nih.gov/pubmed/?term=28350500,, Application
      [Pubmed ID: 30963839], Vera-Escalona I, Habit E, Ruzzante DE, Invasive species and postglacial colonization: their effects on the genetic diversity of a Patagonian fish., Proc Biol Sci, 02-27-2019, https://www.ncbi.nlm.nih.gov/pubmed/?term=30963839,, Application
      [Pubmed ID: 31094605], Schmid M, Dallo R, Guillaume F, Species' Range Dynamics Affect the Evolution of Spatial Variation in Plasticity under Environmental Change., Am Nat, 06-01-2019, https://www.ncbi.nlm.nih.gov/pubmed/?term=31094605,, Application
      This email will never be published. This email is used only for verification and communication purposes.
      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).