Dataset Information

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.

SUBMITTER: Yilmaz P

PROVIDER: S-EPMC3965112 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

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The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks.

Yilmaz Pelin P Parfrey Laura Wegener LW Yarza Pablo P Gerken Jan J Pruesse Elmar E Quast Christian C Schweer Timmy T Peplies Jörg J Ludwig Wolfgang W Glöckner Frank Oliver FO

Nucleic acids research 20131128 Database issue

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 t ...[more]

PMID: 24293649

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Dataset Information

The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks.

Publications

The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks.

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