2. After generating 2,000 haplotypes, the haplotypes were sorted by frequency. Then, starting with haplotype number 200, the disease allele was inserted into the haplotypes until the summed frequency of those haplotypes was equal to the population disease gene frequency. This was an attempt to model disease alleles that came into the population less closely tied to haplotype structure compared to the first method. When the parental genomes were simulated, the haplotypes were chosen randomly, proportional to the frequency of the haplotype in the population. Recombination and gamete production for the genome followed.
