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The NCBI Taxonomy database is curated by a group of taxonomists at the NCBI. They base their curation on the current consensus classification in the scientific literature. The information underlying the classification includes various sequences, like ribosomal RNAs, protein coding genes, concatenated gene trees or whole genome comparisons. However, the classification is not based solely on phylogenetic trees derived from molecular sequences. Although there are a growing number of species with complete genomes in GenBank (INSDC), the vast majority of species in the NCBI Taxonomy database are represented by a small amount of sequence data that are not sufficient to construct a robust phylogeny. Hence, biologists also use morphological comparisons and other more traditional approaches in classifying their studied organisms.

The Taxonomy Common Tree viewer is a tool that allows users to build an abbreviated view of the taxonomic hierarchy for a selected set of organisms. The Common Tree is simply a different display of the Taxonomy records, using the same classification.