...

• Click a Taxonomic data node
• Choose Alpha & beta diversity from the Metagenomic section of the toolbox
• (optional) If you wish to compare the alpha diversity values between groups of samples, choose the factors to set up the ANOVA. This can be helpful if you want to see if there is a significant difference in species diversity between predefined groups. This is optional, so you can skip this if you want.
• Click Finish

...

To obtain the table of pairwise comparisons (dissimilarity matrix) for each distance metric, click the appropriate hyperlink below the Data viewer.  The table will be downloaded as a tab-delimited text file. For both distance metrics, the values range from 0 to 1. The higher the value, the more different that pair of samples are. The lower the value, the more similar they are.

...