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Defining groups

The MLST data used by eBURST are the STs and their associated allelic profiles. The first step is to divide the input data (e.g. the isolates within a MLST database) into groups of STs that have some user-defined level of similarity in allelic profile, since eBURST focuses on those STs that are similar and which may share descent from the same founding genotype, and provides no information about the more distant relationships between groups.

The definition of the group can be changed, but the default eBURST setting is to identify groups of related STs using the most stringent (conservative) definition, where all members assigned to the same group share identical alleles at = 6 of the 7 loci with at least one other member of the group. A less stringent approach is to define the groups by the sharing of alleles at = 5 of the 7 loci. Whatever group definition is used, this approach results in non-overlapping groups; no ST can be assigned to more than one group.

A ’group’ is used here as a neutral term for the collection of STs that are placed together by eBURST, according to the selected group definition, whereas a clonal complex is a set of STs that are all believed to be descended from the same founding genotype. Using the stringent group definition (6/7 shared alleles), isolates in the group defined by eBURST will be considered to belong to a single clonal complex. With a less stringent group definition (e.g. 5/7 shared alleles) all of the STs in an eBURST group cannot be assumed to belong to a single clonal complex.

The eBURST applet is designed for MLST data, which typically uses seven loci, but there is an option to change the number of loci, and the number of shared alleles used to define a group can also be changed to an appropriate number within the applet window.