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Coalescent simulators | Population genomics

Coalescent simulation is pivotal for understanding population evolutionary models and demographic histories, as well as for developing novel analytical methods for genetic association studies for DNA sequence data. A plethora of coalescent…
Migraine
Desktop

Migraine

Allows likelihood analysis of genetic data. Migraine is a software which…

Allows likelihood analysis of genetic data. Migraine is a software which implements coalescent algorithms for maximum likelihood analysis of population genetic data, with a focus on the inference of…

SITES
Desktop

SITES

Analyzes comparative DNA sequence data. SITES is a computer program primarily…

Analyzes comparative DNA sequence data. SITES is a computer program primarily intended for data sets with multiple closely related sequences. It is especially useful when multiple sequences have been…

Infusion
Desktop

Infusion Inference Using Simulation

Implements functions for simulation-based inference. Infusion is a software…

Implements functions for simulation-based inference. Infusion is a software which is aimed to construct an estimation of likelihood surfaces for summary statistics, from which likelihood ratio…

NeEstimator
Desktop

NeEstimator

Provides three single-sample estimators and standard temporal method.…

Provides three single-sample estimators and standard temporal method. NeEstimator is suitable for empirical and simulated datasets containing varying numbers of nuclear genotypes consisting of two or…

Bacter
Desktop

Bacter

Facilitates joint Bayesian inference of ancestral recombination graphs (ARG)…

Facilitates joint Bayesian inference of ancestral recombination graphs (ARG) and related parameters from bacterial sequence alignments under the ClonalOrigin model. Bacter is a BEAST 2 package which…

MCLEEPS
Desktop

MCLEEPS Monte Carlo Likelihood for Estimation of Effective Population Size

Computes the likelihood with data on multiallelic markers. MCLEEPS uses an…

Computes the likelihood with data on multiallelic markers. MCLEEPS uses an importance sampling method to compute the likelihood for the population genetics parameter Ne, given data on temporal…

Coala
Desktop

Coala

An R package for calling coalescent simulators with a unified syntax. Coala can…

An R package for calling coalescent simulators with a unified syntax. Coala can execute simulations with several programs, calculate additional summary statistics and combine multiple simulations to…

SimBac
Desktop

SimBac

Simulates genome wide bacterial evolution. SimBac implements a coalescent-based…

Simulates genome wide bacterial evolution. SimBac implements a coalescent-based algorithm and includes a general model of bacterial recombination that can describe any mixture of within-species and…

msprime
Desktop

msprime

Provides an implementation of Hudson’s algorithm. msprime provides an ms…

Provides an implementation of Hudson’s algorithm. msprime provides an ms compatible command line interface along with a Python API. This implementation uses a simple linked-list based…

BestHet
Desktop

BestHet

Estimates expected heterozygosity in samples containing related and inbred…

Estimates expected heterozygosity in samples containing related and inbred individuals of arbitrary ploidy. BestHet uses a general unbiased linear estimator of allele frequency. It was applied to…

phylodyn
Desktop

phylodyn

Facilitates phylodynamic inference and analysis based on gene genealogies.…

Facilitates phylodynamic inference and analysis based on gene genealogies. phylodyn’s main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time.…

FastSimBac
Desktop

FastSimBac

Models bacterial recombination. FastSimBac is a simulation software that…

Models bacterial recombination. FastSimBac is a simulation software that includes the bacterial sequential Markov coalescent (BSMC) model. The software also includes additional event types: mutation,…

SPLATCHE
Desktop

SPLATCHE SPatiaL And Temporal Coalescences in Heterogeneous Environments

Simulates complex and realistic demographic models and to generate the…

Simulates complex and realistic demographic models and to generate the associated molecular diversity of sampled individuals. Alternative population or environmental histories can be modelled and…

DemoDivMS
Desktop

DemoDivMS

Predicts the genetic diversity at a microsatellite DNA marker, in a finite…

Predicts the genetic diversity at a microsatellite DNA marker, in a finite population, for various mutation models and for variable population size. DemoDivMS is aimed to describe the expected…

ARGON
Desktop

ARGON

A simulator for the discrete time Wright-Fisher model (DTWF) process that…

A simulator for the discrete time Wright-Fisher model (DTWF) process that scales up to hundreds of thousands of samples and whole-chromosome lengths, with a time/memory performance comparable or…

SimRA
Desktop

SimRA Simulation based on Random graph Algorithms

Simulates generic multiple population evolution model with admixture. It is…

Simulates generic multiple population evolution model with admixture. It is based on random graphs that improve dramatically in time and space requirements of the classical algorithm of single…

Cosi
Desktop

Cosi

An efficient simulator that supports both exact and approximate coalescent…

An efficient simulator that supports both exact and approximate coalescent simulation with positive selection. cosi2 improves on the speed of existing exact simulators, and permits further speedup in…

uShuffle
Desktop
Web

uShuffle

Concerns generating uniform random permutations of biological sequences (such…

Concerns generating uniform random permutations of biological sequences (such as DNAs, RNAs, and proteins) that preserve the exact k-let counts. The uShuffle tool implements the latest variant 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…

EvolveAGene
Desktop

EvolveAGene

Simulates the separation of mutation from selection and allows the user to set…

Simulates the separation of mutation from selection and allows the user to set selection conditions. EvolveAGene simulates the evolution of intact coding sequences. It produces realistic data sets…

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…

BaySICS
Desktop

BaySICS Bayesian Statistical Inference of Coalescent Simulations

Performs Approximate Bayesian computation (ABC) analyses by means of coalescent…

Performs Approximate Bayesian computation (ABC) analyses by means of coalescent simulations from DNA sequence data. BaySICS estimates historical demographic population parameters and performs…

Quetzal
Desktop

Quetzal

Provides a set of components to construct coalescence-based simulation…

Provides a set of components to construct coalescence-based simulation programs. Quetzal is an open source modular library which proposes several independent modules for general simulation purpose…

NGSphy
Desktop

NGSphy

Generates next generation sequencing (NGS) data from multiple loci. NGSphy aims…

Generates next generation sequencing (NGS) data from multiple loci. NGSphy aims to improve NGS phylogenomic pipeline. The software allows users to extract information of loci from several…

DIYABCskylinepl…
Desktop

DIYABCskylineplot

Performs an Approximate Bayesian Computation (ABC) skyline plot analysis.…

Performs an Approximate Bayesian Computation (ABC) skyline plot analysis. DIYABCskylineplot is a method to produce ABC from microsatellite data and evaluates its performance on simulated pseudo-data.…

msParSm
Desktop

msParSm

Provides an evolution of msPar, the parallel version of the coalescent…

Provides an evolution of msPar, the parallel version of the coalescent simulation program ms, which removes the limitation for simulating long stretches of DNA sequences with large recombination…

symsim
Desktop

symsim

Allows to study colonization of a new ecological niche. symsim consists in a…

Allows to study colonization of a new ecological niche. symsim consists in a generations model, and each generation represents a population growth, resource competition, and recombination in a…

IRiS
Desktop

IRiS Identification of Recombinations in Sequences

Detects high confidence recombination events in their shared genealogy. IRiS…

Detects high confidence recombination events in their shared genealogy. IRiS assigns an estimated age to each internal node of G. It uses a model-based approach to detecting recombinations in H. The…

scrm
Desktop

scrm

A coalescent simulator for biological sequences. Different to similar programs,…

A coalescent simulator for biological sequences. Different to similar programs, scrm can approximate the Ancestral Recombination Graph as closely as needed, but still has only linear runtime cost for…

MSMS
Desktop

MSMS

A coalescent simulation program for a structured population with selection at a…

A coalescent simulation program for a structured population with selection at a single diploid locus. MSMS includes the functionality of the simulator ms to model population structure and demography,…

MaCS
Desktop

MaCS Markovian Coalescent Simulator

Simulates geneologies spatially across chromosomes as a Markovian process. MaCS…

Simulates geneologies spatially across chromosomes as a Markovian process. MaCS can efficiently simulate haplotypes under any arbitrary model of population history. MaCS produces simulated data that…

IBDsim
Desktop

IBDsim

Simulates genotypic data under general isolation by distance models. IBDSim can…

Simulates genotypic data under general isolation by distance models. IBDSim can consider a large panel of subdivided population models representing discrete subpopulations as well as a large…

GeneArtisan
Desktop

GeneArtisan

A method for simulating samples of marker haplotypes, genotypes, or diplotypes…

A method for simulating samples of marker haplotypes, genotypes, or diplotypes in case-control studies in which the markers are linked to a disease locus in any specified region of the genome. The…

fastsimcoal
Desktop

fastsimcoal

A coalescent-based simulation program which is able to quickly simulate a…

A coalescent-based simulation program which is able to quickly simulate a variety of genetic markers scattered over very long genomic regions with arbitrary recombination patterns under complex…

VarEff
Desktop

VarEff

Estimates the effective population sizes with coalescent approach using…

Estimates the effective population sizes with coalescent approach using microsatellite markers. VarEff is a software which works on steps of constant size to resolve the probabilities by an…

PhyloSim
Desktop

PhyloSim

Can simulate arbitrarily complex patterns of rate variation and multiple indel…

Can simulate arbitrarily complex patterns of rate variation and multiple indel processes, and allows the incorporation of selective constraints on indel events. PhyloSim is an extensible framework…

GONe
Desktop

GONe Generational Overlap Ne

Uses the Jorde-Ryman modification to the temporal method to account for…

Uses the Jorde-Ryman modification to the temporal method to account for age-structure in populations. GONe is a user-friendly, Windows-based program for estimating effective size (Ne) in populations…

BOTTLENECK
Desktop

BOTTLENECK

Detects recent effective population size reductions from allele data…

Detects recent effective population size reductions from allele data frequencies. BOTTLENECK computes for each population sample and for each locus the distribution of the heterozygosity expected…

SIMCOAL
Desktop

SIMCOAL

Allows for simulation of the genomic diversity of samples drawn from a set of…

Allows for simulation of the genomic diversity of samples drawn from a set of populations with arbitrary patterns of migrations and complex demographic histories, including bottlenecks and various…

GFMCMC
Desktop

GFMCMC GLUT for Markov Chain Monte Carlo

Provides a system for visualizing the variables involved in Markov chain Monte…

Provides a system for visualizing the variables involved in Markov chain Monte Carlo (MCMC). GFMCMC is designed to provide a relatively simple user interface that allows management of multiple…

Genepop
Desktop

Genepop

Computes exact tests or their unbiased estimation for Hardy-Weinberg…

Computes exact tests or their unbiased estimation for Hardy-Weinberg equilibrium, population differentiation, and two-locus genotypic disequilibrium. Genepop performs analyses of isolation by…

SNPsim
Desktop

SNPsim

Simulates haplotypes and single nucleotide polymorphims (SNPs) under a modified…

Simulates haplotypes and single nucleotide polymorphims (SNPs) under a modified coalescent with recombination. SNPsim allows for the specification of non-homogeneous recombination rates, which…

SNE
Desktop

SNE Serial NetEvolve

Generates DNA sequences evolved along a tree or recombinant network. Serial…

Generates DNA sequences evolved along a tree or recombinant network. Serial NetEvolve is a modification of the Treevolve program with the following additional features: simulation of serially-sampled…

GENIE
Desktop

GENIE GENealogy Interval Explorer

A framework for inferring the demographic function from reconstructed…

A framework for inferring the demographic function from reconstructed phylogenies. GENIE uses two approaches: demographic models and skyline plot. It infers demographic history from estimated…

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…

RECOAL
Desktop

RECOAL

A coalescent-based method for the simulation of new haplotype data from a…

A coalescent-based method for the simulation of new haplotype data from a reference population of haplotypes. A coalescent genealogy for the reference haplotype data is sampled from the appropriate…

SelSim
Desktop

SelSim

A program for Monte Carlo simulation of DNA polymorphism data for a recombining…

A program for Monte Carlo simulation of DNA polymorphism data for a recombining region within which a single bi-allelic site has experienced natural selection. SelSim allows simulation from either a…

ms
Desktop

ms

A Monte Carlo computer program is available to generate samples drawn from a…

A Monte Carlo computer program is available to generate samples drawn from a population evolving according to a Wright-Fisher neutral model. The program assumes an infinite-sites model of mutation,…

msHOT
Desktop

msHOT

Both crossover and gene conversion hotspots have been incorporated into an…

Both crossover and gene conversion hotspots have been incorporated into an existing coalescent-based program for simulating genetic variation data for a sample of chromosomes from a population.

GENOME
Desktop

GENOME

Proposes a rapid coalescent-based approach to simulate whole genome data. In…

Proposes a rapid coalescent-based approach to simulate whole genome data. In addition to features of standard coalescent simulators, the program allows for recombination rates to vary along the…

SC
Desktop

SC Spatial Coalescent simulator

Facilitates the estimation and description of recombination in population…

Facilitates the estimation and description of recombination in population genomics and evolutionary biology. SC is a method of modeling coalescence with recombination which considerably improved the…

Recodon
Desktop

Recodon

Simulates coalescent simulation of intracodon recombination and of coding DNA…

Simulates coalescent simulation of intracodon recombination and of coding DNA sequences with recombination, migration and demography. Recodon allows to simulate samples of coding DNA sequences under…

AQUASPLATCHE
Desktop

AQUASPLATCHE

A program to simulate genetic diversity based on a realistic vectorized…

A program to simulate genetic diversity based on a realistic vectorized environment. AQUASPLATCHE starts by dividing a realistic vectorized network of river streams into segments of arbitrary length.…

mbs
Desktop

mbs

Generates samples of DNA sequences when there is a biallelic site targeted by…

Generates samples of DNA sequences when there is a biallelic site targeted by selection. The mbs software is so flexible that it can incorporate any arbitrary histories of population size changes and…

CoaSim
Desktop

CoaSim

A tool for simulating the coalescent process with recombination and gene…

A tool for simulating the coalescent process with recombination and gene conversion under various demographic models. CoaSim effectively constructs the ancestral recombination graph for a given…

FastCoal
Desktop

FastCoal

Simulates large chromosomal regions, such as those appropriate in a…

Simulates large chromosomal regions, such as those appropriate in a consideration of genome-wide data, in a way that is several orders of magnitude faster than existing coalescent algorithms.…

EggLib
Desktop

EggLib Evolutionary Genetics and Genomics Library

A C++/Python library and program package for evolutionary genetics and…

A C++/Python library and program package for evolutionary genetics and genomics. Main features are sequence data management, sequence polymorphism analysis, coalescent simulations and Approximate…

eShuffle
Desktop

eShuffle

Predicts statistics and distribution of crossovers for (family) DNA shuffling…

Predicts statistics and distribution of crossovers for (family) DNA shuffling under different experimental conditions (e.g., annealing temperature, fragmentation length, DNA concentration, salt…

Mlcoalsim
Desktop

Mlcoalsim Multilocus Coalescent Simulations

Adds important new features to improve methodology (uncertainty and conditional…

Adds important new features to improve methodology (uncertainty and conditional methods for mutation and recombination), models (including strong positive selection, finite sites and heterogeneity in…

Shufflet
Desktop

Shufflet

Generates random shufflings that conserve the exact count of all words equal to…

Generates random shufflings that conserve the exact count of all words equal to or shorter than a given length k. Such words will be referred to as k-lets, or singlets, doublets, triplets, etc.…

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