The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks.
Yilmaz, Pelin 1,*; Parfrey, Laura Wegener 2,3; Yarza, Pablo 4; Gerken, Jan 1,5; Pruesse, Elmar 1,5; Quast, Christian 1; Schweer, Timmy 1; Peplies, Jorg 5; Ludwig, Wolfgang 6; Glockner, Frank Oliver 1,5,*
[Miscellaneous Article] Nucleic Acids Research. 42(D1):D643-D648, January 1, 2014.

(Format: HTML, PDF)

: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources.

(C) Copyright Oxford University Press 2014.