Definitions

A group
is a set of leaf nodes. These kinds of sets are either from saving a query or by hand-marking on a tree by a user. Each of groups are uniquely identified by a group color. Nine colors are used. Two are reserved colors.

Reserved Colors:
Reserved colors are the default query result color which is sky blue and the color for overlapping nodes, which is black.

Terminal Node vs. Leaf Node:
If a user collapses an interior node, this node becomes a terminal node because no children are displayed for this node, while leaf nodes are always the leaf of a tree.

Property vs. Annotation vs. Trait:
These three are treated the same in the context of TreeQ-VISTA application. They are used interchangeably throughout the tutorial and paper. A property/annotation/trait is a pair of a key and a value. Many values can be associated with the same key. For example: DOMAIN = "Archaea".