For the parameter values specified above, three SAP experiments were simulated. In the first, only the target sequences were simulated into draft, and the NN sequences remained as finished sequences. In the second, the NN sequences were converted to simulated draft and the target sequences remained as finished. In the third, both target and NN sequences were simulated into draft. In the second and third cases, all the NNs were run through the draft simulator each time they were chosen, so that the draft sequences (i.e. location and extent of gaps and sequence errors) differ for the same genome among samples. In the first and third cases, the target sequences must be aligned, and WGASA requires that one of the sequences be a finished genome for reference. Thus, for each random sample from the pool of target genomes, one genome was randomly selected to be the finished genome, and so was left as finished sequence, and the other genomes in the sample were replaced with simulated draft sequence (by running through the draft simulator) before alignment. As with NNs, target draft sequences differ for the same genome among samples due to the randomness of the draft simulation each time it is run. In addition, the target genome that is chosen to be the finished, reference genome differs between samples, and the other target genomes in the sample simulation are replaced with simulated draft versions of the actual finished sequences. Then these sequences were aligned using WGASA and the SAP process was run as described above. A total of 1101 stochastic simulations per 'experiment' were performed, requiring $18 min per simulation. Each simulation involved randomly selecting the subset of target and NN sequences to be included, simulating the draft data based on the finished genomes, aligning the target sample, and finally running the DNA Signature Pipeline. There were four combinations examined: (i) finished variola and finished NN, (ii) draft variola and finished NN, (iii) finished variola and draft NN and (iv) draft variola and draft NN, with each of the draft runs repeated for both low and high sequencing error rates. The combination (iv) was also run with intermediate quality simulated draft variola and low-quality simulated draft NNs. In total, there were eight computational experiments for the finished and simulated draft variola data.