Whole genome sequencing-based typing methods have become the gold standard for phylogenetic classifications of bacterial populations. The most common approach is to compare single nucleotide polymorphisms (SNPs) across the core genome of a cohort of isolates. Greater confidence in SNP-based population assignments can be gained by extending this analysis to include the accessory genome. This is often accomplished by comparing allelic differences between isolates using whole genome multi-locus sequence typing (wgMLST). Unfortunately, allele-based methods, like wgMLST, suffer from being highly species-specific, therefore limiting their current application to only commonly studied bacteria. This work aimed to address this limitation by developing an alternative population classification method based on the accessory genome that could be more universally applied, regardless of the bacterial species being studied. This was accomplished by comparing population assignments based on core SNPs to those derived from the phylogenetic analysis of gene presence/absence matrices output by common pangenome assembly software (i.e., Panaroo or Roary).