Minimum spanning tree (MST)

The minimum spanning tree (MST, see CiMC for the Gower and Ross, 1969 reference) is used in the same way, to identify parts of the configuration which do not fully represent the underlying (dis)similarity matrix. All samples are connected on the ordination by a single line, which may branch but never forms a closed loop, chosen to be of minimum ‘length’ – not using the distances on the ordination but summing the associated dissimilarities from the resemblance matrix. Again, whilst generally the line coincides with a natural joining up of the points in the 2-d ordination, the occasional unnatural links (15 to 16, 19 to 14) show the minor stress in the low-d approximation. You should avoid, of course, taking both MST and Join pairs options at the same time!