Published in
Oxford University Press, Nucleic Acids Research, D1(42), p. D643-D648, 2013
DOI: 10.1093/nar/gkt1209
Links
- Oxford University Press
- ORCID
- [www.ncbi.nlm.nih.gov] | PDF
- [citeseerx.ist.psu.edu] | PDF
- [nar.oxfordjournals.org] | PDF
- [europepmc.org] | PDF
- [www.researchgate.net] | PDF
- [www.ncbi.nlm.nih.gov] | PDF
- [www.ncbi.nlm.nih.gov] | PDF
- [nar.oxfordjournals.org] | PDF
Tools
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks
,
Laura Wegener Parfrey,
Pablo Yarza,
Jan Gerken,
Elmar Pruesse,
Christian Quast,
Timmy Schweer,
Jörg Peplies,
Wolfgang Ludwig,
Frank Oliver Glöckner
Full text: Download
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.