GSR: Simulator - Nemo

Basic Package Attributes
AttributeValue
Title Nemo
Short Description 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.
Long Description 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.
Version 2.3.51
Project Started 2006
Last Release 2 years ago
Homepagehttp://nemo2.sourceforge.net/
Citations Guillaume F, Rougemont J, Nemo: an evolutionary and population genetics programming framework., Bioinformatics, 10-15-2006 [ Abstract, cited in PMC ]
GSR CertificationGSR-certified

Accessibility
Documentation
Application
Support

Last evaluated12-05-2018 (682 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataGenotype at Genetic Markers, Diploid DNA Sequence, Haploid DNA Sequence, Mitochondrial DNA,
VariationsBiallelic Marker, Multiallelic Marker, Single Nucleotide Variation, Microsatellite,
Simulation MethodForward-time, Resample Existing Data,
Input
Data TypeAllele Frequencies, Empirical, Saved simulation, Other,
File formatFstat, Program Specific,
Output
Data TypeGenotype or Sequence, Phenotypic Trait, Individual Relationship, Demographic, Mutation, Diversity Measures, Fitness,
Sequencing ReadsOther (Many built-in statistics, such as f-statistics, demographics, etc, check the manual),
File FormatFstat, Genepop, PED, Program Specific, Other (Space-delimited text files that can be read in excell or r),
Sample TypeSibpairs, Trios and Nuclear Families, Extended or Complete Pedigrees, Case-control, Other (Half-sib/full-sib crossing designs),
Phenotype
Trait TypeBinary or Qualitative, Quantitative, Multiple,
DeterminantsSingle Genetic Marker, Multiple Genetic Markers, Sex-linked (For mitochondrial markers only), 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, Admixed Population, User-defined Matrix, Other (Dispersal as an evolving trait),
SpatialityDiscrete Models, Landscape Factors,
Life CycleDiscrete Generation Model, Age structured, Overlapping Generation, User-Defined transition matrices,
Mating SystemRandom Mating, Monogamous, Polygamous, Selfing, Other (Cloning (no fecundation, no cross-over)),
FecundityConstant Number, Randomly Distributed, Individually Determined, Influenced by Environment,
Natural Selection
DeterminantSingle-locus, Multi-locus, Fitness of Offspring, Phenotypic Trait, Environmental Factors,
ModelsDirectional Selection, Balancing Selection, Multi-locus models, Epistasis (Implicit for quantitative traits), Random Fitness Effects, Disruptive, Other (Multivariate stabilizing selection (gaussian selection)),
RecombinationUniform, Varying Recombination Rates,
Mutation ModelsTwo-allele Mutation Model (For all types of traits), k-Allele Model, Infinite-allele Model, Stepwise Mutation Model,
Events AllowedPopulation Merge and Split, Varying Demographic Features, Population Events, Varying Genetic Features, Change of Mating Systems, Other (Change of parameter values during the course of a simulation, for instance: change of selection pressures caused by environmental changes),
OtherPhenogenetic, Polygenic background,
InterfaceCommand-line, Script-based,
Development
Tested PlatformsWindows (Including cygwin), Mac OS X, Linux and Unix,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Application, Support,

The following 24 publications are selected examples of applications that used Nemo.

2019

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 [Abstract]

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 [Abstract]

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 [Abstract]

2017

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 [Abstract]

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 [Abstract]

2013

Yeaman S, Genomic rearrangements and the evolution of clusters of locally adaptive loci., Proc Natl Acad Sci U S A, 05-07-2013 [Abstract]

2012

Guillaume F, Otto SP, Gene functional trade-offs and the evolution of pleiotropy., Genetics, 12-01-2012 [Abstract]

Zhang H, Guillaume F, Engelstädter J, The dynamics of mitochondrial mutations causing male infertility in spatially structured populations., Evolution, 10-01-2012 [Abstract]

2011

Guillaume F, Migration-induced phenotypic divergence: the migration-selection balance of correlated traits., Evolution, 06-01-2011 [Abstract]

Yeaman S, Whitlock MC, The genetic architecture of adaptation under migration-selection balance., Evolution, 07-01-2011 [Abstract]

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 [Abstract]

2009

Jaquiéry J, Guillaume F, Perrin N, Predicting the deleterious effects of mutation load in fragmented populations., Conserv Biol, 02-01-2009 [Abstract]

Guillaume F, Perrin N, Inbreeding load, bet hedging, and the evolution of sex-biased dispersal., Am Nat, 04-01-2009 [Abstract]

Yeaman S, Guillaume F, Predicting adaptation under migration load: the role of genetic skew., Evolution, 11-01-2009 [Abstract]

Whitlock MC, Guillaume F, Testing for spatially divergent selection: comparing QST to FST., Genetics, 11-01-2009 [Abstract]

2008

Reuter M, Lehmann L, Guillaume F, The spread of incompatibility-inducing parasites in sub-divided host populations., BMC Evol Biol, 05-06-2008 [Abstract]

2007

Guillaume F, Whitlock MC, Effects of migration on the genetic covariance matrix., Evolution, 10-01-2007 [Abstract]

2006

Guillaume F, Perrin N, Joint evolution of dispersal and inbreeding load., Genetics, 05-01-2006 [Abstract]

Gompert Z, and Buerkle CA, What, if anything, are hybrids: enduring truths and challenges associated with population structure and gene flow, Evolutionary Applications, None [Abstract]

Yeaman S, Gerstein AC, Hodgins KA, and Whitlock MC , Quantifying how constraints limit the diversity of viable routes to adaptation, PLOS Genetics, None [Abstract]

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, None [Abstract]

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, None [Abstract]

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, None [Abstract]

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, None [Abstract]


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