simuPOP – general-purpose individual-based forward-time population genetics simulation environment

simuPOP is a general-purpose individual-based forward-time population genetics simulation environment.

Easy simulations like most models in standard population genetics books can be setup easily, whereas very complicated simulations such as spreading of complex diseases, ancient out-of-africa migrations can be built step by step by adding appropriate operators (objects that work on populations).

The core of simuPOP is a scripting language (Python) that provides a large number of objects and functions to manipulate populations, and a mechanism to evolve populations forward in time. Using this R/Splus-like environment, users can create, manipulate and evolve populations interactively, or write a script and run it as a batch file. Owing to its flexible and extensible design, simuPOP can simulate large and complex evolutionary processes with ease. At a more user-friendly level, simuPOP provides an increasing number of built-in scripts that perform simulations ranging from implementation of basic population genetics models to generating datasets under complex evolutionary scenarios.

Key Features

• Provides three types of modules that use 1, 8 or >=32 bits to store an allele.
• Supports autosome, chromosome X, chromosome Y, and mitochondrial chromosomes as a special case of a group of customized chromosome types.
• An arbitrary number of float numbers, called information fields, can be attached to individuals of a population.
• No limit on number of homologous sets of chromosomes, the size of the genome, or the number of individuals in a population.
• Provides more than 70 operators that cover all important aspects of genetic studies:
  • Mutation (k-allele, stepwise, generalized stepwise and hybrid).
  • Migration (arbitrary, can create new subpopulation).
  • Recombination and gene conversion (uniform or nonuniform, sex-specific).
  • Quantitative trait (single, multilocus or hybrid).
  • Selection (single-locus, additive, multiplicative or hybrid multi-locus models).
  • Penetrance (single, multi-locus or hybrid).
  • Ascertainment (case–control, affected sibpairs, random, nuclear and large pedigree).
  • Statistics calculation (including but not limited to allele, genotype, haplotype, heterozygote number and frequency; expected heterozygosity; di-allelic and multi-allelic , and linkage disequilibrium measures).
  • Pedigree tracing.
  • Visualization (using R or other Python modules).
  • Load/save in simuPOP’s native format and many external formats such as Linkage.
• Scripting interface.
• Comprehensive documentation.

Website: bopeng.github.io/simuPOP
Support: GitHub Code Repository
Developer: Bo Peng
License: GNU General Public License v3.0

simuPOP is written in C++. Learn C++ with our recommended free books and free tutorials.

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