PAPA (package for the analysis of parental allocation): a computer program for simulated and real parental allocation

PAPA is a parental pair allocation and simulator program. The allocation method is based on the likelihood of a parental pair producing the multilocus genotype found in the offspring being tested, which will be referred to as the breeding likelihood. Estimated level and structure of allele transmission errors in offspring are parameters fed into the allocation procedure. The embodied Monte-Carlo simulator also allows modelling of many allocation conditions, including transmission error and the estimated proportion of missing parents. Simulations may be run prior to the collection of real parents in order to define the minimal set of loci that is necessary to reach a desired level of allocation success. Post-collection simulations aim at statistically assessing the reliability of nonsimulated allocations. Simulations output values for several random variables.