Reduction of OTU complexity in phylogenetic trees with TreeTrimmer. (A) A phylogenetic tree of mitochondrial Cytochrome c oxidase subunit 2 protein sequences with support values. (B) A trimmed reference tree (cladogram) derived from analysis of the tree shown in A, generated using the first rank of the taxonomic category ‘Eukaryota’ to assess whether all the OTUs belong to the same category in each highly supported clade. The extent of OTU reduction (i.e., dereplication) is shown in boxes. The number in the closed circle indicates the support value in the original tree. (C) Results showing the tree in A pruned with different parameter settings, in this case with the second rank of eukaryotic OTUs, i.e., a more ‘fine-scale’ evolutionary depth. As in B, the tree is shown as a cladogram.