RDP Classifier 2.2 README file
Last update: 03/31/2010
Author: Qiong Wang at wangqion@msu.edu
	James R. Cole at colej@msu.edu
	James M. Tiedje at tiedjej@msu.edu

INTRODUCTION

The RDP Classifier is a naive Bayesian classifier which was developed to provide rapid taxonomic placement based on rRNA sequence data. The RDP Classifier can rapidly and accurately classify bacterial 16s rRNA sequences into the new higher-order taxonomy proposed by Bergey's Trust. It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The RDP Classifier is not limited to using the bacterial taxonomy proposed by the Bergey's Manual. It worked equally well when trained on the NCBI taxonomy. The RDP Classifier likely can be adapted to additional phylogenetically coherent bacterial taxonomies.   

UPDATES:

1. The hierarchy model is updated to training set No. 6, with only minor updates comparing to No. 5, which is based on the nomenclatural taxonomy and Bergey's Manual, 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.

2. Added sanity check code in the training package to make sure taxon name and rank together is unique in the input file that contains the hierarchical taxonomy information.

3. The command line parameters remains the same as version 2.1. It offers three different formats (all tab delimited) based on users' requests:
       allrank: outputs the results for all ranks applied for each sequence: seqname, orientation, taxon name, rank, confidence, ...
       fixrank: only outputs the results for fixed ranks in order: no rank, domain, phylum, class, order, family, genus
       db: outputs the seqname, trainset_no, tax_id, confidence. This is good for storing in a database

4. The version 2.2 contains command line tools to compare two libraries (LibCompare as offered on RDP website). 

The minimum sequence length is remained to be 50 bases due to short reads produced by pyrosequencing technique.  The online version of the Classifier and LibCompare and more help are available on RDP web site: http://rdp.cme.msu.edu/.


FILES

                   
rdp_classifier-2.2.jar
  The compiled RDP Classifier library with training data No. 5 (see above).
  There are three command line demo classes:
  A command line class to create training information from the raw data.
	java -Xmx1g -cp rdp_classifier-2.2.jar edu/msu/cme/rdp/classifier/train/ClassifierTraineeMaker

  A command line class to do the classification. It can use either the sample training data or user specified data.
	java -Xmx1g -jar rdp_classifier-2.2.jar
	ex: java -Xmx1g -jar rdp_classifier-2.2.jar -q sampledata/testQuerySeq.fasta -o ../temp/out.txt -f fixrank

  A command line class to do the library comparison between two input files. 
	java -Xmx1g -cp rdp_classifier-2.2.jar  edu/msu/cme/rdp/classifier/comparison/ComparisonCmd	

sampledata/ 
  A README file about how to train the classifier and classify query sequences.
  Sample raw training data files (testTaxonForQuerySeq.txt and testQuerySeq.fasta)
  and sample property file (rRNAClassifier.properties) 

docs/index.html
  The javadoc.

src/
  The source code.

lib/
  Third party libraries.
