Method | Approach | Reference | Primary result | Secondary result |
---|---|---|---|---|
cgMLST | Alignment to scheme of core genes | Set of allele sequences for set of core genes | Allele distance matrix | Minimum-spanning tree |
wgMLST | Alignment to scheme of core and accessory genes | Set of allele sequences for set of core and accessory genes | Allele distance matrix | Minimum-spanning tree |
SNP | Mapping to reference | Closely related reference genome | Core SNP alignment, SNP distance matrix | Neighbor-joining tree |
Maximum- likelihood tree | ||||
split K-mer based SNP detection | Pairwise K-mer comparison | No reference | Core SNP alignment, SNP distance matrix | Neighbor-joining tree |
MinHash | Pairwise MinHash comparison and clustering | No reference | MinHash distances, clustering information | Neighbor-joining tree |