To display your proximity matrix, just click the Display Prox button on the toolbar.  The result for the Proteins case study looks like this:

This is the Proteins proximity matrix, with 10 clusters highlighted.  We have shaded the within-cluster proximities in blue, and the between-cluster proximities in red.

Note that we show strong similarities with heavy shading, and light or no shading to indicate weak similarities.  This helps you decide whether a particular partition captures all the strong similarities as clusters (perhaps the insects should be clustered on this illustration?)

Why are the colours different?  We selected new colours from the Tree Settings palette, to show off our features..