The IntSim software package has been developed to simulate various genome mutations including germline and somatic variations from next generation sequencing data, and also to generate read data from mixed genomes by considering moderate levels of tumor purity.
SMARTPOP (Simulating Mating Alliances as a Reproductive Tactic for Populations) is a fast and flexible forward-in-time simulator for population genetics. Specially developed for speed, it is available in serial and parallel versions. Developed for anthropological inference on human populations, SMARTPOP simulates individuals with sequences of sex-linked DNA (mitochondria, X and Y chromosomes) and autosomes. Studies of social dynamics are enabled using flexible demographic models and social rules of mating.
MaCS is a simulator of the coalescent process that simulates geneologies spatially across chromosomes as a Markovian process. The algorithm is similar to the SMC algorithm (McVean and Cardin, Phil Trans Soc R B 2005) in that the algorithm scales linearly in time with respect to sample size and sequence length. However, it more accurately models the true coalescent, while supporting all demographic scenarios found in the popular program MS (Hudson, Bioinformatics 2002) making this program appropriate for simulating data for structured populations in genome wide association studies.
TESD simulates the number of genomic TE copies in different populations across generations (according to the Island Model), using classical models of TE dynamics. The parameters of the models (transposition and excision rates, selection intensity, recombination rate, migration rate, population sizes and number of populations) are defined by the users.
NFsim (Network Free Stochastic Simuloator) is a free, open-source, biochemical reaction simulator designed to handle systems that have a large or even infinite number of possible molecular interactions or states. NFsim also has advanced and flexible options for simulating coarse-grained representations of complex nonlinear reaction mechanisms.
NFsim is ideal for modeling polymerization, aggregation, and cooperative reactions that cannot be handled with traditional stochastic or ODE simulators. Models are specified in the BioNetGen Langauge, providing a powerful model building environment.
SVEngine (Structural Variants Engine) is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios.