Given a fasta file of aligned 16S rRNA sequences and a count file generated by Mothur, this tool assigns sequences to taxonomic units (~ species).
Reference (bacterial, full) [bacterial]
Number of iterations (10-1000) 
Remove lineages (empty)
Assigns aligned 16S rRNA sequences to taxonomic units using the Wang method and the Silva reference set (full or just the bacterial references) and its taxonomy file. When using the Silva reference you should be aware of their dual-use license: Silva is free for academic users, but commercial users need to purchase a license.
The bootstrap confidence score is calculated with 100 iterations by default. This low number of iterations is used as a default to make the tool faster, please consider using higher number (1000 for example).
With the Remove lineages parameter you can remove unwanted organisms/sequences from the data. List the unwanted lineages in the text field, for example: Chloroplast-mitochondria-Archaea-Eukaryota-unknown.
This tool is based on the classify.seqs and remove.lineage commands of the Mothur package.
The analysis output consists of the following:
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.