Founderv6 is a population genetics forward simulation that simulates and tracks the heterozygosity of an oscillating population size (per generation) and allows mating system to change incrementally over time. It was written to support our research into sorghum genomes over time. In the sorghum system the mating system changes from 40% inbreeding in the wild progenitor to 80% inbreeding in modern landraces. Currently the script is well annotated to explain the command line inputs, but there is no readme document. In brief there are 11 command line inputs:

1. population size
2. bottleneck size
3. starting number of alleles
4. number of founder events (for this read generations)
5. model of allele frequency generation (choose option 1)
6. mating strategy (expressed as proportion inbreeding)
7. delta mating strategy (the amount by which the mating strategy changes each generation)
8. µ (mutation rate)
9. fast option (choose 1 for fast option, 0 for not)
10. starting heterozygosity (the heterozygosity of the progenitor population - requires option 1 on input 5)
11. starting mating strategy (mating strategy of progenitor population (requires option 1 on input 5)

The programs have been run under the MacOSX perl environment. The founder simulation and it's associated wrap to run multiple simulations can be downloaded from here:

• founderv6 
• founderv6_wrap