Greengenes: Chimera-checked 16S rRNA gene database and workbench compatible in ARB

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Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance (2012, methodology): “Reference sequences were aligned to the GreenGenes core set [29] with PyNAST [30] and masked with the GreenGenes lanemask.”
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers (2008, methodology): “Unique near full-length 16S rRNA sequences were aligned using the NAST web tools (22) and the Greengenes Core Set (17) (12 January 2008 release).”
Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing (2012, background): “Beginning with a phylogenetic tree of cyanobacterial small subunit rRNA genes gathered from the greengenes database (7), cultured strains representative of major cyanobacterial branches for which genome sequences were not yet available were chosen for this”
Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis (2011, methodology): “three widely used curated taxonomy outlines that contain significant conflicts with each other (4).”