User guide

Quantity One User Guide
19-18
The Min. and Max. sliders are active only for proportionally aligned
Neighbor Joined trees. They allow you to adjust the Minimum and Maximum
distance values between nodes on branches, so that you can adjust the
display of your tree to highlight specific regions of data. Distances below the
Min. or above the Max. values will be collapsed to fit on the form.
The Clusters option allows you to define the number of clusters (0 to 18) that
will be identified in your tree for any non-Neighbor Joined tree. Entering a
value greater than zero in this field will cause the tree to redisplay into
separate clusters, identified by letters.
19.4.c Similarity Matrix
The Similarity Matrix contains the similarity values of all of the lanes in a gel.
If there are N lanes in the gel, then the similarity matrix is an N by N matrix
that is computed using the Dice Coefficient as described at the beginning of
this section.
The matrix has the following properties:
• The diagonal elements always have values of 100. This is because a lane is
always 100 percent similar to itself.
• The matrix is symmetrical (M
ij
= M
ji
).
Select Similarity Matrix from the Reports menu to open this report.