SimCopy is an R package simulating the evolution of copy number profiles along a tree. It relies on the PhyloSim package for performing the simulations by encoding the genomic regions as sites in sequences and using modified processes acting on them.
indel-Seq-Gen (iSG) is a biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies. This is accomplished through the addition of subsequence length constraints and lineage- and site-specific evolution. iSG tracks insertion and deletion processes that occur during the simulation run. iSG records all evolutionary events and outputs the “true” multiple alignment of the sequences, and can generate a larger simulated sequence space by allowing the use of multiple related root sequences. iSG can be used to test the accuracy of multiple alignment methods, evolutionary hypotheses, ancestral protein reconstruction methods, and protein superfamily classification methods.
SPIP (simulate pedigrees in populations) simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user. Numerous variables controlling the age structure of the population, the number of offspring produced, the variance in male and female reproductive success, survival rates of different age classes, mate fidelity, duration of simulation, etc. can be specified by the user.
Bugsville simulates the genetics of a quantitative character. The user can breed ladybugs to estimate the heritability of spot number, then conduct a selective breeding experiment to see if the heritability multiplied by the selection differential predicts the response to selection.
AlleleA1 simulates evolution at a single locus in an ideal population of imaginary organisms. The locus of interest has 2 alleles: A1 and A2. The user enters values for parameters controlling selection, mutation, migration, genetic drift, and inbreeding. As the simulation runs, the software plots a graph showing the frequency of allele A1 over time.
Bugs is a simple genetic algorithm program that simulates bacteria-like organisms which move about in a field of “algae” that they eat by moving over them. When they eat enough of the algae, they reproduce by division; if they don’t eat enough, they die. Over time, the initial aimless bugs will evolve into efficient foragers scouring their world for fresh algae.