The nbc_tax command is an implementation of the RDP Naive Bayesian Classifier algorithm (Wang et al. 2007). Predictions by nbc_tax are very similar to the Java implementation provided by RDP; differences are consistent with the randomness of bootstrapping so I believe that the results are equivalent for all practical purposes..
Taxonomy predictions are written to the -tabbedout file. The first three fields are (1) query sequence label, (2) prediction with bootstrap values and (3) strand. If the -sintax_cutoff option is given then predictions are written a second time after applying the confidence threshold, keeping only ranks with high enough confidence. The sintax_summary command can be used to generate a summary report.
The -rdpout output file is compatible with the output generated by the RDP command-line version. This option is provided for the convenience of scripts already written for that program.
The strand option must be specified.
Multithreading is supported.
usearch -nbc_tax otus.fa -db ref16s.fa -strand plus -tabbedout tax.txt
Wang,Q. et al. (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. AEM 73, 5261-7.