Genpax analysis was created for the real-world problem from the bottom-up with scalability as an essential requirement. Scalability is a constraint for existing solutions, the three main reasons being: • The statistical nature of relationship determinations that are impossible to scale (they are ‘NP-hard’ problems) • The loss of resolution with increasing diversity and number of compared strains with common genome SNP • Data generated with more than one reference genome when

When strains are evolving at 1 to 10 nucleotides per year per genome, it is important to address as much of the genome sequence information as possible within the limits of what can be achieved accurately. This cannot be 100% of the genome with current sequencing technologies. For example, regions that are repeatedly present in the genome either identically or with minor variations (for example the ribosomal RNA sequences) are inherently difficult to address. Exactly how much

With some variation by species and genome size, most bacterial pathogens normally change at a rate of up to 10 SNP changes per genome per year. A clinical outbreak spanning weeks or months will include strains diverging at double this rate but also contain strains that differ by less because 99% of strains replicate without error. Meanwhile, sequencing, assembly, and mapping errors can generate tens of errors per MB, resulting in noise that exceeds the essential signal to ide