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Table 1 Phylogenetic approaches

From: Typing methods based on whole genome sequencing data

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