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• rdp-classifier rdp_classifier_2.0.1 file released: rdp_classifier_2.0.1.tar.gz

  Previous release would classify sequences with no valid words. Changed to require new variable MIN_GOOD_WORDS and set it to be MIN_SEQ_LEN - Sequence.WORDSIZE.

  posted 293 days ago

• File released: /rdp-classifier/rdp_classifier_2.0.1/rdp_classifier_2.0.1.tar.gz

  posted 293 days ago

• rdp-classifier rdp-classifier v2.0 file released: rdp_classifier_2.0.tar.gz

  The version 2.0 has only minor changes over the version 1.0. The minimum sequence length is reduced to 50 bases due to short reads produced by pyrosequencing technique. The Hierarchy is now based on the new phylogenetically consistent higher-order bacterial taxonomy (TOBA Release 7.7) proposed by Garrity et. al, with additional major rearrangements that have been proposed for the Firmicutes and Cyanobacteria. It also includes published informal classifications for well-defined lineage with few cultivated members, such as Acidobacteria, Verrucomicrobia and OP11. Additional information for the classification of chloroplasts, Korarchaeota, and Nanoarchaeum were taken from the NCBI taxonomy.

  posted 493 days ago

• File released: /rdp-classifier/rdp-classifier v2.0/rdp_classifier_2.0.tar.gz

  posted 493 days ago

• Training Data Training Data 4, May 2008 file released: RDPClassifier_train052008.tar.gz

  posted 529 days ago

• File released: /Training Data/Training Data 4, May 2008/RDPClassifier_train052008.tar.gz

  posted 529 days ago

• RDP Classifier 1.0 released

  The RDP Classifier is a nave Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. More information can be found at http://rdp.cme.msu.edu/. Environmental gene library analysis has become a mainstream tool in microbial ecology due to the rapid improvements in high-throughput sequencing technology. The small-subunit rRNA gene is often targeted for library construction because of its uses as a phylogenetic marker and in bacterial identification. However, tools for simple and rapid identification of the large numbers of sequences have been lacking. Here we present a nave Bayesian classifier (RDP Classifier) which can rapidly and accurately classify bacterial 16s rRNA sequences into the new higher-order taxonomy proposed by Bergeys Trust. It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The RDP Classifier is suitable both for analysis of single rRNA sequences and for analysis of libraries of thousands of sequences. This Classifier is fast, does not require sequence alignment and works well with partial sequences. The Classifier and related software were written in Java (API v1.4.1) and have been tested on the Solaris (2.8), Linux (2.4.23) and Macintosh (OS 10.3) operating systems using Java virtual machines from Sun and Apple. The compiled RDP Classifier library includes the data from Bergey's bacterial taxonomy outline release 5.0 as the default trained data. To run the Classifier with the default settings, simply provide a file with one or more bacterial 16S rRNA sequences in FASTA, Genbank or EMBL format. The classification results will be written to an output file. The RDP Classifier is not limited to using the bacterial taxonomy proposed by the Bergey's editors. It worked equally well when trained on the NCBI taxonomy. Two files are needed to train the Classifier: one taxonomy file describing the relationships between the taxa, and another file containing trusted seqeunces, each labeled with taxonomic assignments, from domain to genus level. To continue improving RDP Classifier, we now need your help in testing them. Please download the package and try to use it. Please contact rdpstaff@msu.edu or (517) 432-4998 if you have any questions or suggestions. This research was supported by the Office of Science (BER), U.S. Department of Energy, Grant No. DE-FG02-99ER62848 and the National Science Foundation, Grant No. DBI-0328255.

  posted by wangqion 1088 days ago

• rdp-classifier 1.0 file released: rdp_classifier.tar.gz

  posted 1088 days ago

• File released: /rdp-classifier/1.0/rdp_classifier.tar.gz

  posted 1088 days ago

• Code committed

  Anonymous committed patchset 1 of module CVSROOT to the RDP Classifier CVS repository, changing 11 files

  posted by nobody 1096 days ago