GSR: Simulator - quantinemo 2

Basic Package Attributes
AttributeValue
Title quantinemo 2
Short Description A swiss knife to simulate complex demographic and genetic scenarios, forward and backward in time.
Long Description QuantiNemo 2 is a stochastic simulation program for quantitative population genetics. It was developed to investigate the effects of selection, mutation, recombination and drift on quantitative traits and neutral markers in structured populations connected by migration and located in heterogeneous habitats. A specific feature is that it allows to switch between an individual-based full-featured mode and a population-based, faster mode. Several demographic, genetic and selective parameters can be finetuned in QuantiNemo 2: population, selection, trait(s) architecture, genetic map for QTL and/or markers, environment, demography, and mating system are the main features.
Version 2.0.0
Project Started 2018
Last Release 1 year, 7 months ago
Homepagehttps://www2.unil.ch/popgen/softwares/quantinemo/
Citations Neuenschwander S, Michaud F, Goudet J, QuantiNemo 2: a Swiss knife to simulate complex demographic and genetic scenarios, forward and backward in time., Bioinformatics, 03-01-2019 [ Abstract, cited in PMC ]
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Last evaluated07-11-2019 (464 days ago)
Author verificationThe basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataGenotype at Genetic Markers, Diploid DNA Sequence, Sex Chromosomes,
VariationsBiallelic Marker, Multiallelic Marker, Single Nucleotide Variation, Microsatellite,
Simulation MethodStandard Coalescent, Exact Coalescent, Forward-time, Other,
Input
Data TypeAllele Frequencies, Empirical, Saved simulation,
File formatArlequin, Fstat, NEXUS,
Output
Data TypeGenotype or Sequence, Phenotypic Trait, Individual Relationship, Demographic, Diversity Measures, Fitness,
Sequencing ReadsOther,
File FormatArlequin, Fstat, NEXUS,
Sample TypeRandom or Independent, Extended or Complete Pedigrees,
Phenotype
Trait TypeBinary or Qualitative, Quantitative, Multiple,
DeterminantsSingle Genetic Marker, Multiple Genetic Markers, Sex-linked, Gene-Gene Interaction, Environmental Factors, Gene-Environment Interaction,
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, Carrying Capacity, User Defined,
Gene FlowStepping Stone Models, Island Models, Continent-Island Models, Sex or Age-Specific Migration Rates, Influenced by Environmental Factors, User-defined Matrix, Other,
SpatialityDiscrete Models,
Life CycleDiscrete Generation Model,
Mating SystemRandom Mating, Monogamous, Polygamous, Selfing, Other,
FecundityConstant Number, Randomly Distributed, Individually Determined, Influenced by Environment, Other,
Natural Selection
DeterminantSingle-locus, Multi-locus, Fitness of Offspring, Phenotypic Trait, Environmental Factors,
ModelsDirectional Selection, Balancing Selection, Multi-locus models, Epistasis, Random Fitness Effects, Phenotype Threshold,
RecombinationUniform, Varying Recombination Rates,
Mutation ModelsTwo-allele Mutation Model, k-Allele Model, Stepwise Mutation Model, Heterogeneity among Sites,
Events AllowedPopulation Merge and Split, Varying Demographic Features, Population Events, Varying Genetic Features, Change of Mating Systems, Other,
Other
InterfaceCommand-line,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationDocumentation, Application, Support,

No example publication using quantinemo 2 has been provided.

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