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Here a taxonomic identity is assigned to each representative sequence. The taxonomies are pulled from a reference set. There are three main reference databases with aligned, validated and annotated 16S rRNA genes: GreenGenes, Ribosomal Database Project (RDP) and Silva. Each of these databases has strengths and weaknesses that need to be taken into consideration, and all are in common use. Several methods for assigning taxonomy against these reference databases exist, including UCLUST, the RDP classifier and RTAX.

Databases: SILVA, GreenGenes, RDP

Software: UCLUST, the RDP classifier, RTAX