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Classify sequences according to a taxonomy corresponding to a reference taxonomy using one of several methods


  • fasta (fasta file for input sequences)
  • template (fasta file for template database)
  • taxonomy (the taxonomy file for the database)
  • search (values=blast, kmer, suffix; kmer default)
  • method (values=knn and bayesian; default bayesian)
  • ksize (default = 8)
  • match, mismatch, gapopen, gapextend (options for blast search)
  • cutoff (confidence cutoff; default=0.00)
  • numwanted (number of sequences to use in knn method; default = 10)
  • processors (number of processors to use; default = 1)


  • taxonomy (each sequence is followed by a string indicating its taxonomy)
  • tax.summary (a textual hierarchy tree indicating the number of sequences that belong to each level of the hierarchy)

KNN and Bayesian methods modeled from algorithms in Naı¨ve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy􏰎† Qiong Wang,1 George M. Garrity,1,2 James M. Tiedje,1,2 and James R. Cole1* Center for Microbial Ecology1 and Department of Microbiology and Molecular Genetics,2 Michigan State University, East Lansing, Michigan 48824 Received 10 January 2007/Accepted 18 June 2007