Tools to investigate how demographic parameters, populations genetics and abiotic conditions affect the rate of adaptation
http://www.katja-schiffers.eu/research.html

A Simulation Framework for Genome Evolution
http://www.cbrg.ethz.ch/alf

ART is a set of simulation tools to generate synthetic next-generation sequencing data by mimicking real sequencing process with empirical error models or quality profiles.
http://www.niehs.nih.gov/research/resources/software/biostatistics/art/

Methods for realistic simulation of mutations in real data.
https://github.com/adamewing/bamsurgeon

Bayesian Serial SimCoal, (BayeSSC) is a modification of SIMCOAL 1.0, a program written by Laurent Excoffier, John Novembre, and Stefan Schneider.
http://www.stanford.edu/group/hadlylab/ssc/index.html

An integral platform with a graphical interface for statistical inference based on approximate Bayesian computation.
https://sites.google.com/site/baysicsabc/

BEERS was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data
http://cbil.upenn.edu/beers/

Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies
http://www.ensam.inra.fr/urlb/bottleneck/bottleneck.html

BottleSim is a computer simulation program for simulating the process of population bottlenecks
http://chkuo.name/software/bottlesim.html

Protein Sequence Simulation
https://liberles.cst.temple.edu/software/cass/index.html

CDPOP is a landscape genetics tool for simulating the emergence of spatial genetic structure in populations resulting from specified landscape processes governing organism movement behavior.
http://cel.dbs.umt.edu/cdpop

Web-based simulation software
http://www.cgslab.com/

CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models.
http://users-birc.au.dk/mailund/coasim/index.html

The cosi package is written in C and is available as a tar file.
http://www.broadinstitute.org/~sfs/cosi/

A program to simulate the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny
http://bioserv.rpbs.univ-paris-diderot.fr/software/cs-pseq-gen/

An application designed to simulate the evolution of recombinant DNA sequences in continuous time
http://scit.us/projects/dawg

EASYPOP is an individual based model intended to simulate datasets under a very broad range of conditions
http://www.unil.ch/dee/en/home/menuinst/softwares--dataset/softwares/easypop.html

EggLib is a C++/Python library and program package for evolutionary genetics and genomics.
http://egglib.sourceforge.net/

EpiSIM: simulation of multiple epistasis, linkage disequilibrium patterns and haplotype blocks for genome-wide interaction analysis
https://sourceforge.net/projects/episimsimulator/files/

A simulation test bed for hypotheses of genome evolution
http://acb.qfab.org/acb/evolsim/

A realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions
http://bellinghamresearchinstitute.com/software/index.html

A continuous-­‐time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios
http://cmpg.unibe.ch/software/fastsimcoal/

Simulation of Marker and Phenotype Data in Pedigrees
https://watson.hgen.pitt.edu/

C++/Python library for population genetics.
http://webdav.tuebingen.mpg.de/ffpopsim/

The Flux Simulator aims at providing a deterministic in silico reproduction of the experimental pipelines for RNA-Seq, employing a minimal set of parameters.
http://sammeth.net/confluence/display/sim/home

Forward-in-time simulation of Recombination, Quantitative Traits, and Selection
https://bitbucket.org/dkessner/forqs

ForSim: A Forward Evolutionary Computer Simulation
http://anth.la.psu.edu/research/weiss-lab/research/research

The program given below is based on the algorithm described in Padhukasahasram et al. 2008 to simulate genetic drift in a standard Wright-Fisher process.
http://badri-populationgeneticsimulators.blogspot.com/

Forward Population Genetic simulation
https://bio.cst.temple.edu/~hey/software/software.htm#fpg

FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations.
http://www.ebi.ac.uk/projects/bargen

FIGG is a genome simulation tool that uses known or theorized variation frequency, per a given fragment size and grouped by GC content across a genome to model new genomes in FASTA format while tracking applied mutations for use in analysis
http://insilicogenome.sourceforge.net/

A C++ template library for implementing efficient forward simulations.
http://molpopgen.github.io/fwdpp/

Genetic Architecture Model Emulator for Testing and Evaluating Software: Simulates complex SNP models with pure, strict epistatic interactions with n-loci.
http://sourceforge.net/projects/gametes/?source=navbar

Genometric Analysis Simulation Program. A software tool for testing and investigating methods in statistical genetics by generating samples of family data based on user specified models.
http://research.nhgri.nih.gov/gasp/

Genome-wide Complex Trait Analysis
http://www.complextraitgenomics.com/software/gcta/download.html

Next generation sequencing read simulator
http://sourceforge.net/projects/gemsim/

Simulation of Markers in Case-Control Study Designs
http://www.rannala.org/?page_id=241

A rapid coalescent-based whole genome simulator
http://www.sph.umich.edu/csg/liang/genome/

GenomePop2 is a specialization of the program GenomePop just to manage SNPs under more flexible and useful settings. If you need models with more than 2 alleles please use the GenomePop program version.
https://ritchielab.psu.edu/research/research-areas/statistical-genetics-and-gen-epi/methods/genomesimla

GenomeSIMLA is currently under development- however, we have a beta release that we are asking to be tested
http://chgr.mc.vanderbilt.edu/genomesimla/

Simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions.
https://sourceforge.net/projects/gensim/

A rapid whole genome simulation program
http://biostat.mc.vanderbilt.edu/wiki/main/gwasimulator

An association simulator for candidate regions or genome scans
http://www.hapsample.org/

A simulator for the simulation of case control datasets at SNP markers
https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html

A simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients
http://cran.r-project.org/web/packages/hapsim/index.html

A program that simulates heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model
http://l.web.umkc.edu/liujian/

IBDSim is a computer package for the simulation of genotypic data under general isolation by distance models.
http://raphael.leblois.free.fr/

A biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies
http://bioinfolab.unl.edu/~cstrope/isg/

A powerful and flexible simulator of biological evolution
http://abacus.gene.ucl.ac.uk/software/indelible/

InvertFREGENE is a forward-in-time simulator of inversions in population genetic data
http://www.ebi.ac.uk/projects/bargen/

A spatially explicit population genetic simulation engine
http://cran.r-project.org/src/contrib/archive/kernelpop/

Markovian Coalescent Simulator
http://www-hsc.usc.edu/~garykche/

Marlin provides a user-friendly interface for performing forward-in-time population genetic simulations.
http://www.patrickmeirmans.com/software/marlin.html

A package for the simulation of nucleotide data.
http://www.seqan.de/projects/mason/

modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection
http://www.sendou.soken.ac.jp/esb/innan/innanlab/software.html

Mendel's Accountant (MENDEL) is an advanced numerical simulation program for modeling genetic change over time and was developed collaboratively by Sanford, Baumgardner, Brewer, Gibson and ReMine
http://mendelsaccount.sourceforge.net/

Simulates genetics in large size metapopulations
https://sites.google.com/site/marcoandrello/metapopgen

A tool to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets
http://ab.inf.uni-tuebingen.de/software/metasim/

Multilocus Coalescent Simulations
http://code.google.com/p/mlcoalsim-v1/

The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets.
http://home.uchicago.edu/~rhudson1/source/mksamples.html

The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets.
http://home.uchicago.edu/~rhudson1/

A coalescent Simlation tool with selection.
http://www.mabs.at/ewing/msms/index.shtml

A program for the simulation of DNA sequence evolution across a phylogenetic tree
http://www.rosenberglab.net/software.html

A forward-time, individual-based, genetically explicit, and stochastic simulation program designed to study the evolution of genetic markers, life history traits, and phenotypic traits in a flexible (meta-)population framework.
http://nemo2.sourceforge.net/

Coalescent simulation of coding DNA sequences with recombination (inter and intracodon), migration and demography
http://code.google.com/p/netrecodon/

BioConductor package for Forward Genetic Simulation of Cancer Progresion with Epistasis
https://github.com/rdiaz02/oncosimul

Software for simulating eco-evolutionary population dynamics
https://bcrc.bio.umass.edu/pedigreesoftware/node/5

A tool to add phenotypes to simulated genotypes
http://evoplant.uni-hohenheim.de/doku.php?id=software:software

An R package for the Monte Carlo simulation of sequence evolution
http://www.ebi.ac.uk/goldman-srv/phylosim/

Profile-based Illumina pair-end reads simulator
https://code.google.com/p/pirs/

Simulation of protein evolution along phylogenies under structure-based substitution models
http://code.google.com/p/proteinevolver/

QTL and Marker Simulator
http://www.aps.uoguelph.ca/~msargol/qmsim/

An individual-based program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population
http://www2.unil.ch/popgen/softwares/quantinemo/

Simulates new haplotype data from a reference population of haplotypes.
ftp://popgen.usc.edu/

Coalescent simulation of coding DNA sequences with recombination, migration and demography
http://code.google.com/p/recodon/

A package for simulating RNA-seq library preparation with parameter estimation
http://bit.ly/rlsim-git

Rmetasim is a front-end for the metasim engine that is implemented as a package that runs in the statistical computing environment R
http://cran.r-project.org/web/packages/rmetasim/index.html

RSS takes SAM alignment files from RNA-Seq data and simulates over dispersed, multiple replica, differential, non-stranded RNA-Seq datasets.
http://useq.sourceforge.net/cmdlnmenus.html#rnaseqsimulator

Random model of sequence evolution
http://bibiserv.techfak.uni-bielefeld.de/rose/

A coalescent simulator optimized for long sequences and large samples.
https://scrm.github.io/

SelSim is a program for Monte Carlo simulation of DNA polymorphism data for a recom- bining region within which a single bi-allelic site has experienced natural selection
http://www.well.ox.ac.uk/~spencer/selsim/

An application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees.
http://tree.bio.ed.ac.uk/software/seqgen/

Statistical power analysis for sequence-based association studies
http://bioinformatics.org/spower/

SeqSIMLA can simulate sequence data with user-specified disease and quantitative trait models. Family or unrelated case-control data can be simulated.
http://seqsimla.sourceforge.net/

A flexible utility for generating serially-sampled sequences along a tree or recombinant network
http://biorg.cis.fiu.edu/sne/

SFS_CODE can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects.
http://sfscode.sourceforge.net/sfs_code/index/index.html

Quantitative phenotype simulation in extended pedigrees
http://sourceforge.net/projects/sibsim/

A spatially explicit, individual-based, forward-time, landscape-genetic simulation model combined with a landscape cellular automaton.
https://www.openabm.org/model/3137

A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models
http://cmpg.unibe.ch/software/simcoal2/

An R package simulating the evolution of copy number profiles along a tree.
http://bit.ly/simcopy

SIMLA is a SIMuLAtion program that generates data sets of families for use in Linkage and Association studies.
http://dmpi.duke.edu/simla-simulation-software-version-32

A Simulation Program to Generate Haplotype and Genotype Data for Pedigree Structures
http://bioinformatics.org/simped/

A program to simulate protein evolution by substitution, insertion and deletion
http://www.uhnresearch.ca/labs/tillier/software.htm#3

Rare variant simulation and analysis tool
http://code.google.com/p/simrare/

A forward-time simulator that simulates realistic samples for genome-wide association studies.
http://simupop.sourceforge.net/cookbook/simugwas

simuPOP is a general-purpose individual-based forward-time population genetics simulation environment.
http://simupop.sourceforge.net/

A software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices.
http://www.cibiv.at/software/sissi/

Simulating Mating Alliance as a Reproductive Tactic for Populations
http://smartpop.sourceforge.net/

Coalescent simulation of hotspot recombination
http://code.google.com/p/phylosoftware/

SPIP simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user
http://swfsc.noaa.gov/textblock.aspx?division=fed&id=3434

Spatial and Temporal Coalescences in Heterogeneous Environment
http://www.splatche.com/

Simulator of Rare Varaints (srv) is a simulator for the simulation of the introduction and evolution of (rare) genetic variants.
http://simupop.sourceforge.net/cookbook/simurarevariants

SLINK/FastSLINK utility program
http://mlemire.freeshell.org/software.html

A flexible, forward-time population genetic simulator
http://code.google.com/p/treesimj/

A simulation tool for post-GWAS genetic epidemiological studies using whole-genome or whole-exome next-gen sequencing data, with an emphasis on user-friendliness and reproducibility.
http://varianttools.sourceforge.net/simulation/homepage

VORTEX is an individual-based simulation model for population viability analysis (PVA).
http://www.vortex9.org/vortex.html

Whole Exome Sequencing SIMulator
http://sak042.github.io/wessim/