Distance Metrics

A Distance Metric (in the context of MicrobeTrace) is an objective mathematical measurement of the difference between two sequences. MicrobeTrace computes two: SNPs and TN93, but can accept link datasets containing any other.

SNPs

SNP stands for single-nucleotide polymorphism. This metric represents the number of single-nucleotide polymorphisms which would be required to transform one sequence into another (assuming the two are well-aligned). In other words, it is a simple Hamming distance between the two sequences.

TN93

TN93 is the default distance metric for MicrobeTrace. TN93 stands for Tamura-Nei 1993, itself a short reference to a seminal paper.

K Tamura, M Nei; Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees., Molecular Biology and Evolution, Volume 10, Issue 3, 1 May 1993, Pages 512–526, https://doi.org/10.1093/oxfordjournals.molbev.a040023