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Biom.info (version 1.39.5.0)

Biom input dataset:

label - OTU Labels:

Enter a distance label to be used in the shared file created from your biom file (e.g. 0.03)

Summary type:

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, where 105 is the total number of sequences whose otu classified to Clostridiales. Now for basis=otu could give Clostridiales 3 7, where 7 is the number of otus that classified to Clostridiales.

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 biom.info command reads a biom file creates a shared file. If your biom file contains metadata mothur will also create taxonomy or constaxonomy along with tax.summary files.