Note: MIRU-VNTR typing optionally combined with spoligotyping provide(s) the greatest discriminatory power. Therefore, MIRU-VNTR plus spoligo data are especially suited for identification of close relatives by similarity search. However, for tree-based phylogenetic identification we recommend using MIRU-VNTR data, best based on 24 loci, and SNPs or LSPs if available, but not spoligotyping. Spoligo data frequently shows homoplasy problems, while significantly less problems are seen with MIRU-VNTR data and almost none with LSP and SNP data (Allix-Beguec et al., JCM 2008; Comas et al., PloS One 2009). Nevertheless, a posteriori visualisation of corresponding spoligotypes on the tree can be used for further analysis of lineage assignation, based on known informative spoligotype signatures.