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.
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.
| Popular series | |
|---|---|
 | The largest compilation of the best free and open source software in the universe. Each article is supplied with a legendary ratings chart helping you to make informed decisions. |
 | Hundreds of in-depth reviews offering our unbiased and expert opinion on software. We offer helpful and impartial information. |
 | Replace proprietary software with open source alternatives: Google, Microsoft, Apple, Adobe, IBM, Autodesk, Oracle, Atlassian, Corel, Cisco, Intuit, and SAS. |
 | Awesome Free Linux Games Tools showcases a series of tools that making gaming on Linux a more pleasurable experience. This is a new series. |
 | Machine Learning explores practical applications of machine learning and deep learning from a Linux perspective. We've written reviews of more than 40 self-hosted apps. All are free and open source. |
 | New to Linux? Read our Linux for Starters series. We start right at the basics and teach you everything you need to know to get started with Linux. |
 | Alternatives to popular CLI tools showcases essential tools that are modern replacements for core Linux utilities. |
 | Essential Linux system tools focuses on small, indispensable utilities, useful for system administrators as well as regular users. |
 | Linux utilities to maximise your productivity. Small, indispensable tools, useful for anyone running a Linux machine. |
 | Surveys popular streaming services from a Linux perspective: Amazon Music Unlimited, Myuzi, Spotify, Deezer, Tidal. |
 | Saving Money with Linux looks at how you can reduce your energy bills running Linux. |
 | Home computers became commonplace in the 1980s. Emulate home computers including the Commodore 64, Amiga, Atari ST, ZX81, Amstrad CPC, and ZX Spectrum. |
 | Now and Then examines how promising open source software fared over the years. It can be a bumpy ride. |
 | Linux at Home looks at a range of home activities where Linux can play its part, making the most of our time at home, keeping active and engaged. |
 | Linux Candy reveals the lighter side of Linux. Have some fun and escape from the daily drudgery. |
 | Getting Started with Docker helps you master Docker, a set of platform as a service products that delivers software in packages called containers. |
 | Best Free Android Apps. We showcase free Android apps that are definitely worth downloading. There's a strict eligibility criteria for inclusion in this series. |
 | These best free books accelerate your learning of every programming language. Learn a new language today! |
 | These free tutorials offer the perfect tonic to our free programming books series. |
 | Linux Around The World showcases usergroups that are relevant to Linux enthusiasts. Great ways to meet up with fellow enthusiasts. |
 | Stars and Stripes is an occasional series looking at the impact of Linux in the USA. |