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During outbreak investigations and routine surveillance, it is important to be able to identify close genomic relationships, which may indicate a common source, in order to aid in further epidemiological investigations. Fundamentally this relies upon alignment to a reference genome and identification of SNPs (small nucleotide polymorphisms). These sequence alignments can be used to calculate the distances between isolates as a representation of the degree of genomic relatedness. The identification of genomic relationships that inform epidemiological investigations is often a species and context specific process. There are many methods that have been proposed to assess the degree of genomic relationships, including phylogeny-based, Bayesian analysis, hierarchical clustering or combinations of these.