RDP Resource Download Area
Please take a moment to review our License Agreement before downloading any data from our site.
- RDP Tools Repository
- Current release alignments
- Posters and Presentations
- User Submitted Resources
RDP Tools Repository -- Run RDP Tools Locally
Install RDP tools to your local computer, available from GitHub https://github.com/rdpstaff
(RDP Aligners, Classifier, Clustering, FrameBot, GFClassify, Initial Process, KmerFilter, ProbeMatch, ReadSeq, SequenceMatch, SOAP-examples, Xander-HMMgs)
For the pre-compiled RDP Classifier and FrameBot command line tools and training data, visit Sourceforge:
http://sourceforge.net/projects/rdp-classifier/files/ and http://sourceforge.net/projects/rdpframebot/
The current training files and pre-built models for Infernal 1.1 are available here RDP 11 Aligner.
The RDP Paired-end Reads Assembler used in the publication Cole et al., 2014 is available here RDP Paired-end Reads Assembler.
This version provides built-in quality filtering and more command-line options using the RDP algorithm than the one available on the original Pandaseq GitHub repository.
Note: if you run the Assembler program downloaded from the original Pandaseq GitHub repository, specify command-line option "-A rdp_mle" to use RDP's algorithm, and option "-C min_readqscore:25" to filter any assembled reads with Read Q score less than 25.
The most current RDP Classifier training sets (including 16S rRNA, fungal 28S, Warcup fungal ITS and UNITE fungal ITS) are available. We also provides WIU Fungal ITS training set used in the publication Porras-Alfaro et al., 2014 is available here WIU Fungal ITS Classifier training set.
|Gene||Aligned FASTA||Unaligned||Coverage Chart|
|Bacteria 16S||Aligned||Fasta, Genbank||Excel|
|Archaea 16S||Aligned||Fasta, Genbank||Excel|
|Fungal 28S||Aligned||Fasta, Genbank||Excel|
Details of sequence quality check by RDP is available.
These files were compressed using gzip. Common decompression programs should be able to decompress these files. Mac OS X and Linux should have built in support for gzip. Windows users may consider the free and open source decompression program 7-Zip.
The aligned files will unzip to 2-30 GB in size. Lack of available disk space is the most commonly encountered problem when decompressing these files.
Surveys:RDP Survey Results
Posters and Presentations:
These posters were presented by the RDP at the International Society for Microbial Ecology Biennial Symposia.
These posters were presented by the RDP at the American Society for Microbiology annual meetings.
2015 RDP Poster (3MB pdf)
2015 Xander Poster (3MB pdf)
2014 RDP ppt for ASM Conference for Undergraduate Educators (3.4MB pdf)
2014 RDP Poster (2.7MB pdf)
2013 RDP Poster (2.7MB pdf)
2012 RDP Poster (15MB pdf)
2012 RDP Fungene Poster (15MB pdf)
2011 RDP Poster (15MB pdf)
2010 RDP Poster (17MB pdf)
Slideshow Pyrosequencing-Enabled Large Scale, Rapid and Parallel Analysis of Microbial Community Structure and Functions (ASM Session 203/N, May 19, 2009)
2009 RDP Poster (13MB pdf)
2008 RDP Poster (8MB pdf)
2008 Pyrosequencing Pipeline Poster (8.6MB pdf)
2007 Poster (5.7MB pdf)
2006 Poster (4.3MB pdf)
2005 Poster (3MB pdf)
2004 Poster (1.2MB pdf)
2003 Poster (1.1MB pdf)
2002 Poster (1.6MB pdf)
2001 Poster (1.2MB pdf)
2000 Poster (220KB pdf), Sequence Space supplement (3.2MB pdf), Backbone Tree supplement (62KB pdf)
These posters were presented by the RDP at the Mycological Society of America Annual Symposia.
2014 MSA Poster (3.9MB pdf)
User Submitted Resources:
The following have been submitted by RDP users. Please refer to the original publication for more information.
GenBank accession mappings for sequences used in Kuske's 2007 AEM paper
Click here to download GenBank accession mappings for the 26 groups discussed in
Kuske, S. and S. Barns (2007). Acidobacteria phylum sequences in uranium-contaminated
subsurface sediments greatly expand the known diversity within the phylum. Appl. Environ. Microbiol. 73(9):3113-3116.
To retrieve the sequences from RDP, upload the accessions into your seqCart.
Universally Conserved Genes
Santos, S. R. and Howard Ochman. Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environmental Microbiology. 2004. Jul(6)7:754-9. [PubMed 15186354]
Scott Santos and Howard Ochman (University of Arizona, Tucson) have graciously made the sequence data from their paper available for distribution by the Ribosomal Database Project along with additional genes and sequences developed since publication. Also see RDP's Functional Gene Pipeline and Repository.
|Right Click to Download Files|
|DNA fasta||DNA fasta||DNA fasta||DNA fasta||DNA fasta||DNA fasta||DNA fasta||DNA fasta||DNA fasta|
|DNA nexus||DNA nexus||DNA nexus||DNA nexus||DNA nexus||DNA nexus||DNA nexus||DNA nexus||DNA nexus|
|Protein fasta||Protein fasta||Protein fasta||Protein fasta||Protein fasta||Protein fasta||Protein fasta||Protein fasta||Protein fasta|
|Protein nexus||Protein nexus||Protein nexus||Protein nexus||Protein nexus||Protein nexus||Protein nexus||Protein nexus||Protein nexus|
Philip Hugenholtz's 16S rRNA ARB Database
Hugenholtz, Philip (January 2002) Exploring prokaryotic diversity in the
genomic era. Genome Biology 3(2):reviews0003.1-0003.8
[ http://genomebiology.com/2002/3/2/reviews/0003 (Access to article requires subscription) ]
Release Notes - ARB File (6.3MB)