simuPOP
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.
Features include:
- 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
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Last Updated Saturday, April 13 2013 @ 04:14 PM EDT
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