Galaxy |

Classify.otu (version 1.39.5.0)

list - OTU List :

name - taxonomy sequence names:

count - used to represent the number of duplicate sequences for a given representative sequence:

Select Taxonomy from:

taxonomy - Taxonomy Reference:

label - OTU Labels:

cutoff - Confindence percentage cutoff between 1 and 100:

probs - Show probabilities:

basis - Summary file gives numbers of:

group - Groups for summary file:

persample - allows you to find a consensus taxonomy for each group:

default false

Relative abundance values?:

use relative abundances rather than raw abundances for the tax.summary file

Tax summary output type:

The detail format outputs the totals at each level, where as the simple format outputs the highest level

Print level:

specify taxlevel of your *tax.summary file to print to. Options are 1 to the maz level in the file. The default is -1, meaning max level

Output logfile?:

Mothur Overview

Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki.

Command Documentation

The classify.otu command assigns sequences to chosen taxonomy outline.

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.

v1.21.0: Updated to use Mothur 1.33. Added count parameter (1.28.0) and persample parameter (1.29.0)