The draft SAP simulations are nearly identical to those using finished genomes, described previously (5, 6) . The SAP ( Figure 1 ) performs stochastic (Monte Carlo) simulations and includes our DNA and Protein Signature Pipelines as components, which will be summarized briefly below. It is necessary to describe what the signature pipelines do before the SAP can be clearly described, so signature pipelines will be discussed first. As a step within the DNA and Protein Signature Pipelines, DNA sequence alignments of multiple draft genomes are required. For this we use the WGASA software, also summarized below. Once each of these components of the SAP has been presented, the SAP itself will be described.