PhyloScope Quick Start Guide
About PhyloScope
PhyloScope is a tool for visualization of evolutionary trees. It supports a number of features:
- Interactive user control of information detail
- Linking of leaves to internet resources
- Display of node-specific information by tool tip
- Highlighting of path from mouse-over node to tree root
- Display of edge lengths on mouse-over
- Interactive collapsing of tree nodes
- Coloring of subtrees to show relationships, such as orthology, among leaves
- Selection of subsets of leaves with highlighted spanning subtree
Known browser incompatibilities
There are known problems with user interaction using Internet Explorer, and Phyloscope will not render in Safari 4.0.3. We recommend the use of Firefox or earlier versions of Safari as browsers for viewing trees with PhyloScope. Please avoid using Internet Explorer until these issues are resolved.
PhyloScope functions
Figure 1. The controls for the tree display appear at the top of the PhylosScope window. The user can control the
display of information by clicking on the checkbox next to the information type:
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Figure 2. In this display, each subtree of sequences belonging to the same subfamily has been collapsed to an internal node
indicated by a square. The number in brackets at the node shows the number of sequences in the collapsed subtree:
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Figure 3. When the tree is fully expanded, the subtrees are indicated by color:
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Figure 4. Placing the cursor over an edge in the tree shows the length of that highlighted edge in a tool tip:
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Figure 5. Tool tips are also shown for links that appear in the leaves of the tree. In most cases, a click
will take the user to the internet information resource that is the origin of the information. The path in the tree from
the leaf to the root of the tree is highlighted:
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Figure 6. At subfamily nodes, the tool tip displays summary information for that subtree:
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Figure 7. Clicking on any internal node will collapse the subtree above that node. Information about the subfamily will
be displayed for subfamily nodes:
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Figure 8. When a set of leaves is selected, the leaves and spanning subtree are highlighted.
To aid in finding widely separated leaves on large trees, a graphic is drawn in the right margin that points to all the leaves
in the selected set:
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