In genomics, 16S/18S/ITS gene sequencing (or simply amplicon analysis) is used to identify or classify bacterial species. 16SrRNA is a DNA sequence encoding in a small subunit of rRNA in prokaryotes. It is mainly used to analyze the diversity of bacteria and archaea. 18SrRNA is the same thing, but in eukaryotes, mostly used for its v4 region information abundance. ITS sequencing is mainly used for phylogenetic analysis of fungi. 16SrDNA, 18SrDNA, and ITS sequencing tools are used for experimental design, prediction and homogeny-based taxonomic classification, and data preprocessing.
Metagenomics tools allow population analysis of unculturable or previously unknown microbes. This is important because only about 1-2% of all bacteria can be cultured in a lab. Metagenomics is the study of the functional genomes of microbial communities while amplicon analysis offers a phylogenetic survey on the diversity of a single ribosomal gene.
SILVA is a manually curated database that has taxonomic information for organisms in the Bacteria, Archaea, and Eukarya domains. It can be used for 16SRNA and 18SRNA analysis.
The RDP database is based on 16S rRNA sequences from the aforementioned domains, and includes fungi.
The Greengenes taxonomy is used for the Bacteria and Arachaea domains. A phylogenetic tree is constructed from 16SRNA sequences found from public databases and is passed through a quality filter. Go here for more info.
NCBI is also manually curated and contains the names of all organisms submitted to the NCBI sequence database.