title: The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks.
abstract: 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.
authors.affiliation: Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany, Department of Botany, University of British Columbia, Vancouver V6T 1Z4, Canada, Department of Zoology, University of British Columbia, Vancouver V6T 1Z4, Canada, Ribocon GmbH, D-28359 Bremen, Germany, School of Engineering and Science, Jacobs University Bremen gGmbH, D-28759 Bremen, Germany and Lehrstuhl für Mikrobiologie, Technische Universität München, D-853530 Freising, Germany.
authors.forename: Pelin
authors.initials: P
authors.lastname: Yilmaz
authors.forename: Laura Wegener
authors.initials: LW
authors.lastname: Parfrey
authors.forename: Pablo
authors.initials: P
authors.lastname: Yarza
authors.forename: Jan
authors.initials: J
authors.lastname: Gerken
authors.forename: Elmar
authors.initials: E
authors.lastname: Pruesse
authors.forename: Christian
authors.initials: C
authors.lastname: Quast
authors.forename: Timmy
authors.initials: T
authors.lastname: Schweer
authors.forename: Jörg
authors.initials: J
authors.lastname: Peplies
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Ludwig
authors.forename: Frank Oliver
authors.initials: FO
authors.lastname: Glöckner
mesh_terms: D001105:Archaea / Q000145:classification*; D001419:Bacteria / Q000145:classification*; D030561:Databases, Nucleic Acid; D056890:Eukaryota / Q000145:classification* / Q000235:genetics; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D020459:Genes, rRNA; D020407:Internet; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012338:RNA, Ribosomal, 23S / Q000235:genetics; D016415:Sequence Alignment; D012984:Software; D009626:Terminology as Topic
chemical_list: D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S