The following additional custom scripts were used for the development of MGT for Staphylococcus aureus.
Script 1: Subsets the dataset, such that each ST is sampled proportionally based on that ST's frequency in the species dataset
Script 2: Calculate number of recomination events per locus, and count the number of recombinant regions that overlap.
Script 3: Separates the core loci into preferences, and select core loci to fill the different MGT levels (from MGT2 to MGT7).