Bio-Rad Quantity One 1-D Analysis Software - Manual (Page 227)

Quantity One User Guide
10-18
Options
Click on the Options button in the Phylogenetic Tree window to open the Options
dialog.
Fig. 10-13. Two forms of the Options dialog.
The box on the left has controls that are specific for the Neighbor Joining method.
The box on the right is applicable to the other tree methods. Both boxes share certain
features.
Each allows you to choose between aligning the tree to the right or proportionally
aligning it. Right alignment uses a fixed branch length for displaying the distance
between nodes; proportional alignment differs for Neighbor Joining and other tree
modes.
With the Neighbor Joining method, proportional alignment shows branch length sizes
proportional to the min/max values set in the Options dialog. Other methods plot the
nodes at locations determined by their similarity values.
The Fit Tree in Window option scales the tree so that the entire tree will fit onto a
single printed page. With this turned off, the entire tree will appear with the correct
distances between nodes preserved, and the printed tree can be tiled across multiple
sheets of paper.
The Neighbor Joining Options dialog, click on the Designate New Root button to
designate a new root node (the node at the very top of the tree), enabling you to look
at the relationships between lanes from a different perspective. This will highlight all
the nodes in the tree. Click on the node that you want to serve as the new root and the
Neighbor Joining Only
All Other Methods