1. Haplotypes were sorted, treating the haplotypes as a character string. A group of haplotypes that were similar in structure (that were neighbors after sorting) were chosen to carry the disease allele and the frequency of those haplotypes adjusted to equal the disease gene frequency. This approach was an attempt to model the situation where similar haplotypes carry the disease allele. When the parental genomes were simulated, the haplotypes were chosen randomly, proportional to the frequency of the haplotype in the population, and inserted into the appropriate place in the genome. Recombination and gamete production for the genome followed.
