The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy

  title={The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy},
  author={James R. Cole and Benli Chai and Terry L. Marsh and Ryan J. Farris and Qiong Wang and S. A. Kulam and S. Chandra and Donna M. McGarrell and Thomas M. Schmidt and George M. Garrity and James M. Tiedje},
  journal={Nucleic acids research},
  volume={31 1},
The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (, RDP-II offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences (trees) derived from these data. RDP-II release 8.1 contains 16 277 prokaryotic, 5201 eukaryotic, and 1503 mitochondrial small subunit rRNA sequences in aligned and annotated format. The current public beta… 
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with analysis services and a phylogenetically consistent taxonomic
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The results suggest that 16S rDNA datasets need to be analyzed in multiple ways when being used for community ecology studies, and FastGroupII is an effective bioinformatics tool for the trimming and dereplication of 16 S rDNA sequences.
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atabase resources of the National Center for Biotechnology Information: update
In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in
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Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction.
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Taxonomic Outline of the Prokaryotes
  • Bergey’s Manual of Systematic Bacteriology,
  • 2002
PHYLIP—Phylogeny Inference Package (Version 3.2)
  • Cladistics
  • 1989