User guide

Reports
19-17
Fig. 19-11. Two forms of the Options dialog box.
The box on the left has controls that are specific for the Neighbor Joining
method. The box on the right is applicable to all 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.
In Neighbor Joining mode, proportional alignment shows branch length sizes
proportional to the min./max. values (see below) set in the Options form.
Other modes 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 Fit Tree in Window 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 form allows you 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. You do so by clicking on the
Designate New Root button. This will highlight all the nodes of the tree on-
screen. Choose the one you want to serve as the new root by clicking on it.
The rearranged dendrogram will then be displayed. If you wish to return to
the original form of the tree, click on the Restore Original Tree button.
Neighbor Joining Only
All Other Methods