GenomeSmasher is a set of tools used to create diploid FASTA files with containing snps, indels, duplications, deletions and translocations. These FASTA files can then be used in conjunction with next-generation sequencing simulators to artificially create sequencing experiments. The utility of these tools are to assess the performance and reliability of data analysis in next-generation sequencing pipelines.
gargammel is a set of programs aimed at simulating ancient DNA fragments. For ancient hominin samples our program can also simulate various levels of present-day human contamination and microbial contamination.
The Populus software contains a set of simulations that we use to teach population biology and evolutionary ecology at the University of Minnesota. Simulation models may be chosen from a menu, and students can move among the parameter boxes of an input window, changing initial defaults to values of their own choosing.
alfacinha is a source-package of object-oriented Python modules for sequence evolution allowing for neighbor-dependent substitutions under GPL license.This package is aimed at simulating the evolution of sequences along phylogenetic trees. It provides several modules to store and manipulate evolutionary models, to store and evolve a sequence, and store and manipulate evolutionary trees
EvolSimulator is a program that allows the simulation of evolution at the level of genes, gene families, and whole genomes. It was designed with the goal of investigating evolutionary phenomena like biased mutation regimes in different lineages, complicated patterns of selective pressure across sequences, and the confounding effects of paralogy and lateral genetic transfer.
GEvolutionS simulates an evolutionary Genome rearrangement scenario with different genome rearrange operations. It operates on the most general model of genomes with a mixed collection on linear and circular genomes. The simulation process includes all classical rearrangement operations such as dcj, fissions, fusions, inversions, translocations, transpositions with choosable quantum.