GSR: Simulator - FFPopSim

Basic Package Attributes
AttributeValue
Title FFPopSim
Short Description C++/Python library for population genetics.
Long Description FFPopSim is a C++ and Python library to simulate large populations that are polymorphic at many loci. It allows for complex fitness functions, including pairwise and higher order epistasis. It is designed to study the effects of linked selection, the rare processes in large populations, and can be used to address a large variety of population genetics problems.
Version 2.0
Project Started 2012
Last Release 7 years, 8 months ago
Homepagehttp://webdav.tuebingen.mpg.de/ffpopsim/
Citations Zanini F, Neher RA, FFPopSim: an efficient forward simulation package for the evolution of large populations., Bioinformatics, 12-15-2012 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated11-10-2017 (1072 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence,
VariationsBiallelic Marker,
Simulation MethodForward-time, Phylogenetic,
Input
Data TypeAllele Frequencies, Empirical, Ancestral Sequence, Saved simulation,
File formatProgram Specific,
Output
Data TypeGenotype or Sequence, Phenotypic Trait, Demographic, Linkage Disequilibrium, Diversity Measures, Fitness,
Sequencing ReadsOther,
File FormatProgram Specific,
Sample TypeLongitudinal,
Phenotype
Trait TypeBinary or Qualitative, Quantitative, Multiple,
DeterminantsSingle Genetic Marker, Multiple Genetic Markers, 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 Flow
Spatiality
Life CycleDiscrete Generation Model,
Mating SystemRandom Mating,
FecundityRandomly Distributed,
Natural Selection
DeterminantSingle-locus, Multi-locus, Codon-based, Fitness of Offspring, Phenotypic Trait, Environmental Factors,
ModelsDirectional Selection, Balancing Selection, Multi-locus models, Epistasis, Random Fitness Effects, Disruptive, Phenotype Threshold, Frequency-Dependent, Other,
RecombinationUniform, Varying Recombination Rates,
Mutation ModelsTwo-allele Mutation Model,
Events AllowedPopulation Merge and Split, Varying Demographic Features,
Other
InterfaceCommand-line, Script-based,
Development
Tested PlatformsMac OS X, Linux and Unix,
LanguageC or C++, Python,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation,

No example publication using FFPopSim has been provided.

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