Abstract
Advanced intercross lines (AIL) have proven to be a powerful tool in genetic research to map complex genetic traits. The advantage of AIL is the high enrichment of visible recombination events to fine map the position of the target gene. Therefore, AIL are generated under the avoidance of inbreeding. We developed an online software tool, RANDOMATE, that generates random mating schemes such that only animals from different families are paired. When animals have to be selected randomly for mating, RANDOMATE optimizes the mating scheme such that all families contribute equally to the next generation. RANDOMATE uses a divide-and-conquer algorithm to define a mating scheme without brother-sister matings for all animals of a generation. If not all animals can be considered for the next generation, the mating scheme maximizes the randomness of the occurrences of animals from their families to make the family contributions as equal as possible. RANDOMATE is freely available at http://www2.hu-berlin.de/RandoMate.