Policy Document
 
DATABASES
SUBMISSIONS
NEWS

 

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Subgroups and Subgroup founders

Each ST that has at least two descendent SLVs (a total of three including the SLV that is its progenitor) will under the default definition be assigned as a subgroup founder and coloured yellow. The number of total SLVs that define a subgroup founder can be changed from this default setting and this is strongly recommended for large groups.

In large MLST databases, large groups will often have a single good candidate for the primary founder, as one ST has many more associated SLVs than the other STs, is the most common ST in the dataset, and has strong bootstrap support. In other cases there may be no predicted primary founder and this is likely to occur with small groups. In some cases there may be two STs that each have a considerable number of SLVs, but one has slightly more SLVs (or the same number of SLVs, but one has more DLVs), and therefore is assigned by eBURST as the primary founder. Due to the preferential assignment rule, STs that are subgroup founders may have considerably more SLVs than are shown in the eBURST diagram. The number of SLVs linked to a subgroup founder in an eBURST diagram will therefore typically be less than the true number of SLVs. The correct number of SLVs of any ST is shown in the tabular output (‘Analysis’ window). Where one ST has only slightly more SLVs than another possible primary founder, or when the choice of the primary founder is made only on the number of DLVs, the bootstrap support is likely to be unconvincing, with both STs having moderate support as the primary founder. In such cases, either ST may be the primary founder of the group (or the founder of the group may not be in the dataset) and further information may be required to try and understand the patterns of descent within the eBURST group. eBURST v2 allows any group to be re-drawn with any ST selected as the user-defined primary founder (see section 9.8). The user-defined primary founder is coloured red to distinguish it from the founder chosen by the eBURST algorithm (blue).

Displaying a “Population Snapshot”


The whole input population (e.g., a whole MLST database) can be shown as a single eBURST diagram, to visualise the number and sizes of clusters of linked STs etc. This can be done by setting the group definition in the ‘Analysis Panel’ from the default value of 6/7 to 0/7. This will put all STs in the whole input data into a single eBURST group, and selecting ‘group 1’ in the ‘Diagram Panel’ will display all clusters of STs and unlinked individual STs as a single eBURST diagram – this display is called a “Population Snapshot”. The linked clusters within the population snapshot should represent clonal complexes and the primary founders and subgroups founders of these linked clusters are coloured blue and yellow (See Figure 7).