Fig 1. Examples of clustering definition and growth criteria.

Subtree (A) represents a paraphyletic cluster (C₁) of two background (old) sequences, O₁ and O₃, excluding a third sequence O₂ that is too distance from the root node of C₁. Consequently, O₂ becomes its own cluster of one, C₂. Subtree (B) illustrates a monophyletic cluster where all background sequences meet this criterion. Subtrees (C-E) depict the addition of a new (incident) sequence N to an existing cluster. In (C), the new sequence is added with 100% confidence to a cluster of one background sequence, O₂. Conversely, the placement of N in subtrees (D) and (E) is highly uncertain (with bootstrap supports 40% and 60%). For (D), N becomes incorporated into the same cluster irrespective of its placement, so the bootstrap values are irrelevant. In contrast, neither placement of N in subtree (E) meets the clustering criteria due to the resulting branch lengths—as a result, N becomes a new cluster of one, C₃.