Thus, the SAP performs Monte Carlo sampling from the target and NN genomes, runs each sample through the signature pipeline and summarizes the results of the hundreds of signature pipeline runs in a single plot. On our 24 CPU Sun server, up to seven signature pipeline simulations may be run in parallel, each requiring $15-22 min for viral genomes. All of the SAP analyses of dozens of bacteria and viruses to date have used a total run time of 6.26 years (operating in parallel), with an average pipeline run time of 0.522 h, and a process time span of 2.32 years.