Classify sequences to taxonomic units


Given a fasta file of aligned 16S rRNA sequences and a count file generated by Mothur, this tool assigns sequences to taxonomic units (~ species).



Assigns aligned 16S rRNA sequences to taxonomic units using the Wang method and the Silva reference set 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 parameters you can remove unwanted organisms/sequences from the data. Some common options are provided as yes/no parameters. You can list others in the "Remove other lineages" text field. Use dots (.) instead of semicolons (;) in names. Use dash (-) to separate taxons. For example: Bacteria.Firmicutes.-Bacteria.Bacteroidetes.

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.