GSR: Simulator - quantinemo 2
Attribute | Value |
---|---|
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 | 5 years ago |
Homepage | https://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 ] |
GSR Certification | Accessibility |
Last evaluated | 07-11-2019 (1717 days ago) |
Author verification | The 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. |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Genotype at Genetic Markers, Diploid DNA Sequence, Sex Chromosomes, |
Variations | Biallelic Marker, Multiallelic Marker, Single Nucleotide Variation, Microsatellite, |
Simulation Method | Standard Coalescent, Exact Coalescent, Forward-time, Other, |
Input | |
Data Type | Allele Frequencies, Empirical, Saved simulation, |
File format | Arlequin, Fstat, NEXUS, |
Output | |
Data Type | Genotype or Sequence, Phenotypic Trait, Individual Relationship, Demographic, Diversity Measures, Fitness, |
Sequencing Reads | Other, |
File Format | Arlequin, Fstat, NEXUS, |
Sample Type | Random or Independent, Extended or Complete Pedigrees, |
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, User-defined Matrix, Other, |
Spatiality | Discrete Models, |
Life Cycle | Discrete Generation Model, |
Mating System | Random Mating, Monogamous, Polygamous, Selfing, Other, |
Fecundity | Constant Number, Randomly Distributed, Individually Determined, Influenced by Environment, Other, |
Natural Selection | |
Determinant | Single-locus, Multi-locus, Fitness of Offspring, Phenotypic Trait, Environmental Factors, |
Models | Directional Selection, Balancing Selection, Multi-locus models, Epistasis, Random Fitness Effects, Phenotype Threshold, |
Recombination | Uniform, Varying Recombination Rates, |
Mutation Models | Two-allele Mutation Model, k-Allele Model, Stepwise Mutation Model, Heterogeneity among Sites, |
Events Allowed | Population Merge and Split, Varying Demographic Features, Population Events, Varying Genetic Features, Change of Mating Systems, Other, |
Other | |
Interface | Command-line, |
Development | |
Tested Platforms | Windows, Mac OS X, Linux and Unix, |
Language | C or C++, |
License | GNU Public License, |
GSR Certification | Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using quantinemo 2 has been provided.
Please propose new citations if you are aware of publications that use this software.