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Forward simulators | Population genomics

In population genetics, simulation is a fundamental tool for analyzing how basic evolutionary forces such as natural selection, recombination, and mutation shape the genetic landscape of a population. Forward simulation represents the most powerful,…
SBVB
Desktop

SBVB Sequence-Based Virtual Breeding

Simulates complex traits and genotype data. SBVB is a sequence based population…

Simulates complex traits and genotype data. SBVB is a sequence based population simulator that generates molecular and phenotypic data using real sequence data. The software allows users to specify…

SFS_CODE
Desktop

SFS_CODE Simulating Finite Sites under COmplex Demographic Events

Generates samples from populations with complex demographic histories under…

Generates samples from populations with complex demographic histories under various models of natural selection. SFS_CODE performs simulations under a general Wright-Fisher model with arbitrary…

GeneEvolve
Desktop

GeneEvolve

A simulator to handle life history scenarios and to generate individual-level…

A simulator to handle life history scenarios and to generate individual-level phenotypes and realistic whole-genome sequence for large populations. GeneEvolve runs forward-in-time, which allows it to…

SeDuS
Desktop

SeDuS Segmental Duplication Simulator

A flexible and user-friendly forward-in-time simulator of patterns of molecular…

A flexible and user-friendly forward-in-time simulator of patterns of molecular evolution within segmental duplications undergoing interlocus gene conversion and crossover. SeDuS introduces known…

PReFerSim
Desktop

PReFerSim

A C program that performs forward simulations under the Poisson Random Field…

A C program that performs forward simulations under the Poisson Random Field (PRF) model. PReFerSim models changes in population size, arbitrary amounts of inbreeding, dominance, and distributions of…

Admix'em
Desktop

Admix'em

A forward-time simulator that allows for rapid and realistic simulations of…

A forward-time simulator that allows for rapid and realistic simulations of admixed populations with selection. Complex selection can be achieved through user-defined fitness and mating-preference…

VIRAPOPS
Desktop

VIRAPOPS

Allows RNA virus population simulation. VIRAPOPS is a forward simulator…

Allows RNA virus population simulation. VIRAPOPS is a forward simulator designed to model a real situation such as virus population in a naive or infected patient. The software allows virus…

INDELible
Desktop

INDELible

Provides a flexible and powerful tool for simulating molecular sequence…

Provides a flexible and powerful tool for simulating molecular sequence evolution. INDELible is a portable and flexible application for generating nucleotide, amino acid and codon sequence data by…

Biotools
Desktop

Biotools

Predicts gene diversity over a sampling area. Biotools is an R package that…

Predicts gene diversity over a sampling area. Biotools is an R package that allows users to obtain spatial unbiased estimates of gene diversity from molecular datasets. This program was designed to…

disease sims
Desktop

disease sims

Explores the impact of genetic model and population growth on distribution of…

Explores the impact of genetic model and population growth on distribution of genetic variance across the allele frequency spectrum underlying risk for a complex disease. disease_sims, using…

QuasiFit
Desktop

QuasiFit

Estimates fitness from Next-Generation-Sequencing (NGS) data based on…

Estimates fitness from Next-Generation-Sequencing (NGS) data based on quasispecies theory. QuasiFit infers fitness landscapes from NGS samples of HIV-1 patient-derived viruses, using quasispecies…

Molkin
Desktop

Molkin

Allows to realize several genetic analyses on microsatellite information.…

Allows to realize several genetic analyses on microsatellite information. Molkin is a genetics computer program which assists researchers or responsible to handle large data files such as that…

forqs
Desktop
Nemo
Desktop

Nemo

Provides developers with abstract models allowing them to implement their own…

Provides developers with abstract models allowing them to implement their own life-history traits and life-cycle events. Nemo is an individual-based, genetically explicit and stochastic population…

XSim
Desktop

XSim

Simulates sequence data in descendants in arbitrary pedigrees. The XSim…

Simulates sequence data in descendants in arbitrary pedigrees. The XSim strategy is to drop-down origins and positions of chromosomal segments rather than every allele state is implemented to…

SGWE
Desktop

SGWE Simulation of Genome-Wide Evolution

Simulates genome/proteome-wide evolution under heterogeneous substitution…

Simulates genome/proteome-wide evolution under heterogeneous substitution models and a range of evolutionary scenarios. SGWE simulates this evolution under a variety of substitution models that may…

SeqSIMLA
Desktop

SeqSIMLA

A simulation tool that can simulate sequence data with user-specified disease…

A simulation tool that can simulate sequence data with user-specified disease and quantitative trait models. SeqSIMLA can efficiently simulate sequence data with disease or quantitative trait models…

OncoSimulR
Desktop

OncoSimulR

Addresses a wide range of questions that span from the effect of…

Addresses a wide range of questions that span from the effect of mutator/antimutator genes, to the interplay between fitness landscapes, population sizes and mutation rates. OncoSimulR implements…

Discoal
Desktop

Discoal

Generates population samples that include selective sweeps in a feature-rich,…

Generates population samples that include selective sweeps in a feature-rich, flexible manner. discoal can perform simulations conditioning on the fixation of an allele due to drift or either hard or…

SELAM
Desktop

SELAM Simulation of Epistasis Local adaptation with Ancestry and Mate choice

A forward-time population genetic simulator that is designed to efficiently…

A forward-time population genetic simulator that is designed to efficiently handle both short and long term admixture simulations while retaining complete local ancestry information. SELAM can…

PaGELL
Desktop

PaGELL Parametric Genetic Evaluation of Lifespan in Livestock

Analyzes (right-censored) longevity data in livestock populations, with a…

Analyzes (right-censored) longevity data in livestock populations, with a special emphasis on the genetic evaluation of breeding stock. PaGELL relies on a parametric generalization of the…

Geno-Diver
Desktop

Geno-Diver

Simulates complex traits involving quantitative and/or fitness components.…

Simulates complex traits involving quantitative and/or fitness components. Geno-Diver is a combined coalescence and forward-in-time simulator that implements multiple selection and mating strategies…

SLiM
Desktop

SLiM

Combines putative dependency structures in a weighted manner, allowing for…

Combines putative dependency structures in a weighted manner, allowing for numerical optimization of dependency structure and model parameters simultaneously. Slim is a general-purpose forward…

fwdpp
Desktop

fwdpp

A C++ library of routines intended to facilitate the development of…

A C++ library of routines intended to facilitate the development of forward-time simulations under arbitrary mutation and fitness models. The library design provides a combination of speed, low…

GenomeSIMLA
Desktop

GenomeSIMLA

Generates datasets using a forward-time population simulator which relies on…

Generates datasets using a forward-time population simulator which relies on random mating, genetic drift, recombination, and population growth to allow a population to naturally obtain linkage…

JMating
Desktop

JMating

Analyses mating frequency data to study sexual selection and sexual isolation…

Analyses mating frequency data to study sexual selection and sexual isolation effects from laboratory experiments as well as descriptive studies accomplished in the wild. JMating allows the…

SimAdapt
Desktop

SimAdapt

Represents evolutionary processes of adaptation and population dynamics in…

Represents evolutionary processes of adaptation and population dynamics in changing landscapes, using the NetLogo environment. SimAdapt simulates the evolution of both neutral and adaptive genotypes…

Pydigree
Desktop

Pydigree

Offers a user-friendly environment to develop genetic software. Pydigree allows…

Offers a user-friendly environment to develop genetic software. Pydigree allows users to create and manipulate genetic data. It provides functions for the simulation of both pedigrees and…

Mobsim
Web
Desktop

Mobsim

Allows users to simulate the abundances and the spatial distribution of…

Allows users to simulate the abundances and the spatial distribution of individuals of different species. Mobsim permits users to define key properties of communities, including the total numbers of…

GilchristEtAl20…
Desktop

GilchristEtAl2017

Allows users to study amino acid residue. This method is a quantitative,…

Allows users to study amino acid residue. This method is a quantitative, population genetics based physico-chemical model. It assists in extraction of information from observational data. It consists…

Parallel…
Desktop

Parallel PopGen Package

Allows simulation of allele trajectories and generation of site frequency…

Allows simulation of allele trajectories and generation of site frequency spectrum (SFS). Parallel PopGen Package is a library of three application programming interfaces (APIs): (i) GO Fish that can…

Bacmeta
Desktop

Bacmeta

Allows users to provide simulations about evolution of bacterial genomes in…

Allows users to provide simulations about evolution of bacterial genomes in multiple connected populations. Bacmeta permits to modelize multiple arbitrarily connected populations for which the genome…

FractalSIM
Desktop

FractalSIM

Mimics various population genetics models. FractalSIM is a multi-scenario…

Mimics various population genetics models. FractalSIM is a multi-scenario genome-wide simulation framework that accounts for natural selection pre-and post-admixture processes. It offers users the…

COMPASS
Desktop

COMPASS COMPletely Arbitrary Sequence Simulator

Allows to simulate the evolution of all discrete state space by a tree for all…

Allows to simulate the evolution of all discrete state space by a tree for all form of time-reversible model. COMPASS simulates evolution site-by-site and is easy to parallelize in order to enable…

SpartaABC
Web

SpartaABC

Implements an approximate Bayesian-computation rejection algorithm to infer…

Implements an approximate Bayesian-computation rejection algorithm to infer indel parameters from sequence data. SpartaABC is a web app that extracts a vector of summary statistics from its input; it…

ProBaBool
Desktop

ProBaBool

Simulates heterogeneous populations using Boolean models. ProBaBool is a part…

Simulates heterogeneous populations using Boolean models. ProBaBool is a part of the method that captures both the long-term outcomes of a heterogeneous population, as well as the transient behavior…

popRange
Desktop

popRange

Provides a simulation framework for modeling highly probabilistic spatial and…

Provides a simulation framework for modeling highly probabilistic spatial and temporal population dynamics. Features such as spatially and temporally variable selection coefficients and demography…

SMARTPOP
Desktop

SMARTPOP Simulating Mating Alliance as a Reproductive Tactic for Populations

Facilitates large-scale statistical inference on interactions between social…

Facilitates large-scale statistical inference on interactions between social factors, such as mating systems, and population genetic diversity. SMARTPOP can simulate a wide range of genetic systems…

GENS
Desktop

GENS Gene-Environment iNteraction Simulator

Simulates interactions among two genetic and one environmental factor. GENS…

Simulates interactions among two genetic and one environmental factor. GENS allows for epistatic interactions. It is based on data with realistic patterns of linkage disequilibrium, and imposes no…

MetaPopGen
Desktop

MetaPopGen

Allows modeling of very complex demographic scenarios. MetaPopGen removes the…

Allows modeling of very complex demographic scenarios. MetaPopGen removes the limitations imposed by large population size, which affect individual-based simulation models. It focuses on genotype…

rmetasim
Desktop

rmetasim

A plugin to perform individual-based population genetic simulations. rmetasim…

A plugin to perform individual-based population genetic simulations. rmetasim combines realistic demography, including temporal variation in vital rates, with neutral evolution at multilocus…

Pyvolve
Desktop

Pyvolve

An open-source Python module for simulating sequences along a phylogenetic…

An open-source Python module for simulating sequences along a phylogenetic tree. Pyvolve simulates sequences along a phylogeny using continuous-time Markov models of sequence evolution for…

spaMM
Desktop

spaMM

Fits spatial generalized linear mixed models (GLMMs) in R. spaMM is a software…

Fits spatial generalized linear mixed models (GLMMs) in R. spaMM is a software package based on the iteratively reweighted least squares algorithm for estimation of β with the gradient and Hessian…

GP
Desktop

GP GenomePop

Simulates different Markovian nucleotide or codon models of DNA mutation.…

Simulates different Markovian nucleotide or codon models of DNA mutation. GenomePop has many interesting characteristics to simulate single-nucleotide polymorphism or DNA sequences under complex…

Clotho
Desktop

Clotho

A general method for representing in silico genetic sequences using implicit…

A general method for representing in silico genetic sequences using implicit data structures. Clotho provides a generalized implementation as a C++ template library. It is a general way for improving…

SimBA
Desktop

SimBA Simulation using Best-fit Algorithm

A non-generative method for simulating populations with various specified…

A non-generative method for simulating populations with various specified distributions such as minimum allele frequency (MAF) distribution, linkage disequilibrium (LD) etc. SimBA outperforms the…

I-CBN
Desktop

I-CBN Isotonic Conjunctive Bayesian Network

Estimates both the underlying mutational order constraints and the fitness…

Estimates both the underlying mutational order constraints and the fitness landscape from observed genotype-phenotype data. I-CBN is a general statistical model based that serves for parameter…

EpiSIM
Desktop

EpiSIM Epistasis SIMulator

A software tool that can simulate some of the statistical properties of genetic…

A software tool that can simulate some of the statistical properties of genetic data. EpiSIM is capable of expanding the range of the epistasis models that current simulators offer, including…

Population Lab
Desktop

Population Lab

Provides several models of familial disease aggregation and show that the…

Provides several models of familial disease aggregation and show that the parameters used in the simulations are faithfully estimated. Population Lab is a method and a software package for simulating…

sads
Desktop

sads

Contains features for fitting and comparing probability distributions models to…

Contains features for fitting and comparing probability distributions models to both species abundance distributions (SADs) and species rank abundance distributions (RADs). sads is a R package which…

WH
Desktop

WH

Fits a simple speciation model, called the Isolation Model, to multilocus DNA…

Fits a simple speciation model, called the Isolation Model, to multilocus DNA sequence data sets. WH is a computer program that conducts tests of the quality of fit of that model. With comparative…

invertFREGENE
Desktop

invertFREGENE

Simulates inversion polymorphisms in population genetic data. invertFREGENE has…

Simulates inversion polymorphisms in population genetic data. invertFREGENE has been developed from a beta version of the population genetic simulator FREGENE. The main default of the tool is that…

Mendel
Desktop

Mendel Mendel's Accountant

Investigates the processe of mutation and selection in sexually reproducing…

Investigates the processe of mutation and selection in sexually reproducing diploid populations. In Mendel, as in nature, mutations have a continuous range of effect from lethal to beneficial, and…

SPIP
Desktop

SPIP Simulate Pedigree In Population

Simulates multilocus genetic data on individuals in age-structured populations.…

Simulates multilocus genetic data on individuals in age-structured populations. SPIP allows investigation of the relationship between family structure and population parameters. The tool will be…

quantiNemo
Desktop

quantiNemo

Allows the simulation of genetic and phenotypic data for complex quantitative…

Allows the simulation of genetic and phenotypic data for complex quantitative traits in a realistic and dynamic metapopulation with selective pressures. quantiNemo was developed to investigate the…

TreesimJ
Desktop

TreesimJ

A flexible, easy to use population genetic simulator that tracks the ancestry…

A flexible, easy to use population genetic simulator that tracks the ancestry of the entire population in question. TreesimJ provides many fitness and demographic models and new models are easy to…

GSR
Dataset

GSR Genetic Simulation Resources

A website provided by the National Cancer Institute (NCI) that aims to help…

A website provided by the National Cancer Institute (NCI) that aims to help researchers compare and choose the appropriate simulation tools for their studies. This website allows authors of…

HapSim
Desktop

HapSim

A simulation tool for the generation of haplotype data. The simulated…

A simulation tool for the generation of haplotype data. The simulated haplotypes are such that their allele frequencies and linkage disequilibrium coefficients match exactly those estimated in a real…

simuPOP
Desktop

simuPOP

A forward-time population genetics simulation environment. The core of simuPOP…

A forward-time population genetics simulation environment. The core of simuPOP is a scripting language (Python) that provides a large number of objects and functions to manipulate populations, and a…

EvolSimulator
Desktop

EvolSimulator

Allows the simulation of evolution at the level of genes, gene families, and…

Allows the simulation of evolution at the level of genes, gene families, and whole genomes. EvolSimulator was designed with the goal of investigating evolutionary phenomena like biased mutation…

FFPopSim
Desktop

FFPopSim Fast Forward Population Genetic Simulation

A C++ and Python library to simulate large populations that are polymorphic at…

A C++ and Python library to simulate large populations that are polymorphic at many loci. FFPopSim allows for complex fitness functions, including pairwise and higher order epistasis. It is designed…

ForSim
Desktop

ForSim

A flexible forward evolutionary simulation tool for exploring the consequences…

A flexible forward evolutionary simulation tool for exploring the consequences of evolution by phenotype, whereby demographic, chance, behavioral and selective effects mold genetic architecture.…

PEDAGOG
Desktop

PEDAGOG

Models dynamics of multiple populations and their interactions through…

Models dynamics of multiple populations and their interactions through individual based simulations while simultaneously recording genotype, pedigree, and trait information at the individual level.…

MARLIN
Desktop

MARLIN

A Mac OS X software for performing spatially realistic simulations. MARLIN…

A Mac OS X software for performing spatially realistic simulations. MARLIN improves the workflow of performing population genetic simulations by providing user interface with realistic geographic…

kernelPop
Desktop

kernelPop

Implements almost any arbitrary population-genetic and demographic model in a…

Implements almost any arbitrary population-genetic and demographic model in a spatially explicit context using a variety of dispersal kernels. kernelPop implements biparental inheritance of unlinked…

CDPOP
Desktop

CDPOP Cost Distance POPulations

A spatially-explicit simulator of gene-flow in complex landscapes to explain…

A spatially-explicit simulator of gene-flow in complex landscapes to explain observed population responses and provide a foundation for landscape genetics. The program implements individual-based…

Forwsim
Desktop

Forwsim

An exact forward-in-time algorithm that can efficiently simulate the evolution…

An exact forward-in-time algorithm that can efficiently simulate the evolution of a finite population under the Wright-Fisher model. The authors used simulations based on this algorithm to verify the…

FREGENE
Desktop

FREGENE

A flexible and efficient simulation software and a rescaling technique have…

A flexible and efficient simulation software and a rescaling technique have been developed to aid computational efficiency that together allow the simulation of sequence-level data over large genomic…

HAPSIMU
Desktop

HAPSIMU

Provides a common genetic simulation platform to evaluate the impact of…

Provides a common genetic simulation platform to evaluate the impact of population structure on population-based association studies. HAPSIMU can simulate heterogeneous populations with various known…

EASYPOP
Desktop

EASYPOP

A computer program allowing to simulate population genetics datasets. EASYPOP…

A computer program allowing to simulate population genetics datasets. EASYPOP allows generating genetic data for haploid, diploid, and haplodiploid organisms under a variety of mating systems. It…

Punnett Square…
Desktop

Punnett Square Calculator

Visualizes all the possible combinations of different types of gametes in…

Visualizes all the possible combinations of different types of gametes in particular crosses or breeding experiments. Punnett Square Calculator is a graphical method looks like a two-dimensional…

CASS
Desktop

CASS Coarse-grained Artificial Sequence Simulator

Allows modeling of the interplay between population size, mutation rate and…

Allows modeling of the interplay between population size, mutation rate and selection by simulating a population of virtual organisms, each assigned a fitness value based on folding stability and…

fwdpy
Desktop

fwdpy

Facilitates the development of forward-time simulations under arbitrary…

Facilitates the development of forward-time simulations under arbitrary mutation and fitness models, using fwdpp. fwdpy provides a combination of speed, low memory overhead, and modeling flexibility.…

BottleSim
Desktop

BottleSim

A computer simulation program for simulating the process of population…

A computer simulation program for simulating the process of population bottlenecks. The major novelties of the program include 1) implementation of an overlapping-generation model, 2) ability to…

AnA-FiTS
Desktop

AnA-FiTS Ancestry-Aware Forward-in-Time Simulator

Simulates genetic sequences of a population forward in time under a…

Simulates genetic sequences of a population forward in time under a Fisher-Wright model with selection and dynamically changing population size. The two main aspects of AnA-FiTS are: an…

ALF
Web

ALF Artificial Life Framework

Simulates processes at the genomic level. ALF aims at simulating the entire…

Simulates processes at the genomic level. ALF aims at simulating the entire range of evolutionary forces that act on genomes: nucleotide, codon, or amino acid substitution (under simple or mixture…

FPG
Desktop

FPG Forward Population Genetic

Simulates a population of constant size that is undergoing various evolutionary…

Simulates a population of constant size that is undergoing various evolutionary processes, including: mutation, recombination, natural selection, and migration. The meaning of "forward" in…

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