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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]

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