Figure 8

Online assignment of alleles as resident or foreign. Having assigned a query strain to a species (Figure 7), the locus view page shows the assignment of each of the seven individual sequences as resident to that species (or compatible with being resident) or foreign. In the example, the sequences of five of the genes from strain SK264 are assigned by eMLSA.net as resident (that is, S. parasanguinis) or resident compatible, but the pyk and tuf genes are assigned as foreign. The locus view page allows the individual gene trees (in this case, the tuf tree) to be displayed to explore why the algorithm considers the sequences of an allele of a query strain to be resident, resident compatible or foreign (see Figure 6 for details). The colour codes for species clusters are as in Figure 2.