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  In the tree shown in Figure 12 (genus _Brachybacterium_), our sample of interest from an assembly is "_Brachybacterium muris_ UCD-AY4" \cite{23516213}. It falls within a clade where every named member has the same name "_Brachybacterium muris_", and this name does not occur elsewhere on the tree. Hence, we were confident enough to name our organism as that species. In other words, this sequence falls within a well-supported clade of _Brachybacterium muris_.    In the tree shown in Figure 13 (genus _Tatumella_) our species of interest is _Tatumella_ sp. UCD-D _suzukii_ \cite{24762940}. In contrast to the _Brachybacterium_ example, here our species falls within a poorly defined clade containing multiple species. In this case case,  we did not assign a species name to this isolate.