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The classify.otu command is used to get a consensus taxonomy for an otu.

Default Setting

The classify.otu command parameters are list, taxonomy, name, count, cutoff, label and probs. The taxonomy and list parameters are required.

First you must classify your sequences, you can do so by running the following command:

mothur > classify.seqs(fasta=abrecovery.fasta, template=silva.nogap.fasta, taxonomy=silva.full.taxonomy)

Then you can use your taxonomy file to find the consensus taxonomy for your otus at various distances.

mothur > classify.otu(taxonomy=abrecovery.silva.full.taxonomy, list=abrecovery.fn.list)

When you open abrecovery.fn.0.10.cons.taxonomy you will see:

36	1	Bacteria(100);Firmicutes(100);Clostridiales(100);Ruminococcus_et_rel.(100);Anaerofilum-Faecalibacterium(100);Faecalibacterium(100);Faecalibacterium_prausnitzii(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
37	15	Bacteria(100);Firmicutes(100);Clostridiales(100);Ruminococcus_et_rel.(100);Anaerofilum-Faecalibacterium(100);Faecalibacterium(100);Faecalibacterium_prausnitzii(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
38	17	Bacteria(100);Firmicutes(100);Clostridiales(100);Ruminococcus_et_rel.(100);Anaerofilum-Faecalibacterium(100);Faecalibacterium(100);Faecalibacterium_prausnitzii(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
39	1	Bacteria(100);Firmicutes(100);Clostridiales(100);Ruminococcus_et_rel.(100);Anaerofilum-Faecalibacterium(100);Faecalibacterium(100);Faecalibacterium_prausnitzii(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);

The first column is the otu number, the second column is the number of sequences in the otu and the third column is the consensus taxonomy.


The name parameter allows you add a names file with your taxonomy file.

mothur > classify.otu(taxonomy=abrecovery.silva.full.taxonomy, list=abrecovery.fn.list, name=abrecovery.names) 


The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information.

mothur > classify.otu(taxonomy=abrecovery.silva.full.taxonomy, list=abrecovery.fn.list, count=abrecovery.count_table) 


The cutoff parameter allows you to specify a consensus confidence threshold for your taxonomy. The default is 51, meaning 51%. Cutoff cannot be below 51.

mothur > classify.otu(taxonomy=abrecovery.silva.full.taxonomy, list=abrecovery.fn.list, cutoff=80) 


The label parameter allows you to select what distance levels you would like a output files created for, and is separated by dashes. The default value for label is all labels in your inputfile.

mothur > classify.otu(taxonomy=abrecovery.silva.full.taxonomy, list=abrecovery.fn.list, label=0.10-0.20) 


The probs parameter shuts off the outputting of the consensus confidence results. The default is true, meaning you want the confidence to be shown.

mothur > classify.otu(taxonomy=abrecovery.silva.full.taxonomy, list=abrecovery.fn.list, probs=f) 


The basis parameter allows you indicate what you want the summary file to represent, options are otu and sequence. Default is otu. For example consider the following basis=sequence could give Clostridiales 3 105 16 43 46, where 105 is the total number of sequences whose otu classified to Clostridiales. 16 is the number of sequences in the otus from groupA, 43 is the number of sequences in the otus from groupB, and 46 is the number of sequences in the otus from groupC. Now for basis=otu could give Clostridiales 3 7 6 1 2, where 7 is the number of otus that classified to Clostridiales. 6 is the number of otus containing sequences from groupA, 1 is the number of otus containing sequences from groupB, and 2 is the number of otus containing sequences from groupC.


The group parameter allows you to provide a group file to use when creating the summary file.


The persample parameter allows you to find a consensus taxonomy for each group. Default=false.


The reftaxonomy parameter allows you give the name of the reference taxonomy file used when you classified your sequences. Providing it will keep the rankIDs in the summary file static.


  • 1.28.0 Added count parameter
  • 1.29.0 Added persample parameter
  • 1.29.0 Bug Fix - if basis=sequence and count file is used, redundant sequences were not added to .tax.summary file counts.