Several of my software applications for teaching evolution have served as prototypes for exercises included in the EvoBeaker package from SimBiotic Software. EvoBeaker is a commercial product, but the cost per student is reasonable. And it's worth paying for: The labs have improved functionality, a consistent user interface, and accompanying tutorials that have been extensively tested. A sampler of SimBiotic products is available on request.
I am no longer developing or supporting the applications that have become part of EvoBeaker. They are still available here, however, for those who want to use them.
Jon Herron's Evolution Simulation Software for Evolutionary Analysis
PhyloStrat lets the user explore what happens when species are independently designed versus evolved by descent with modification. It was the prototype for the Flowers and Trees lab in EvoBeaker.
EvoDots lets the user explore the mechanism of evolution. The program creates a population of dots. The user is a predator. As the dots run around the screen, the user eats them by clicking on them with the mouse. After the user has eaten some of the dots, the survivors will reproduce. The population may or may note evolve, depending on the properties of the dots. EvoDots was the prototype for the Darwinian Snails lab in EvoBeaker.
FrogPond challenges the user to design experiments that will establish the cause of deformities in a model frog population.
PopCycle lets the user explore the power of combining Mendelian genetics with Darwinian selection. It was the prototype for the Hardy, Weinberg, and Kuru lab in EvoBeaker.
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.
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.
ForensicEA lets the user explore the logic of phylogeny reconstruction. The program creates populations of virus particles. The populations evolve by genetic drift. The user can sample and complare nucleotide sequences from the populations. Various simulations let the user collect and analyze data on: genetic drift within a single population; divergence of populations by drift; and variation among populations on a known phylogeny. If you like ForensicEA, please take a look at the Domesticating Dogs and HIV Clock labs in EvoBeaker.