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The pca command requires a shared or relabund file.

Default settings

A shared or relabund file must be inputted for pca to be successful.

mothur > pca(shared=genus.pool.shared)


mothur > pca(relabund=genus.pool.relabund)

The output to the screen would look something like:

You did not provide a label, I will use the first label in your inputfile.

Processing genus
Rsq 1 axis: 0.777358
Rsq 2 axis: 0.893548
Rsq 3 axis: 0.953764



The label parameter is used to analyze specific labels in your input. Default is the first label in your shared or relabund file. Multiple labels may be separated by dashes.


The groups parameter allows you to specify which groups you would like analyzed. Groupnames are separated by dashes.


The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True


  • 1.40.0 - Speed and memory improvements for shared files. #357 , #347