The kruskal.wallis command will find the Kruskal Wallis one way analysis of variance for each OTU. To follow along with this tutorial you can download the example files.

Default Setting

The shared and design parameters are required.

mothur > kruskal.wallis(,

The file will look like:

OTULabel    KW  Pvalue
Otu001  0.534545    0.464702
Otu002  0.0981818   0.754023
Otu003  6.81818     0.00902344
Otu004  0.541104    0.461975
Otu005  0.534545    0.464702
Otu006  0.0109091   0.916815



The label parameter allows you to select what distance level you would like. Multiple labels can be separated by dashes.

mothur > kruskal.wallis(,, label=0.03)


If your design file contains multiple categories, you may select the category you would like to use. If you do not select a class the first category will be used.


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