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03. Tips and Nodes
Right-click (or Ctrl-click on a single-button mouse) on any node, branch, or tip to open a context menu. The actions offered depend on what the node represents and the current state of the tree:
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View Subtree: hide everything outside this clade. Available when the node is a valid root for a subtree view (i.e., not the root or a tip), and only when no subtree view is currently active.
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Highlight Clade / Remove Clade Highlight: paint a translucent green band over every descendant of this node to call attention to a clade. The same item toggles between Highlight and Remove depending on whether the clade already has a highlight. You can also toggle this for the currently selected node from the keyboard with the
Lkey.
Note
The highlight color can be changed by hovering your mouse over the highlighted node and selecting a key between 1 and 6.
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Root Here: re-root the tree on the branch leading to this node. Available only when the node is a valid potential outgroup and no subtree view is active.
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Drop This Node: remove the node (and the clade beneath it) from the tree. Available only when the node can be safely removed without invalidating the tree.
If you right-click on the dashed handle that appears between the tree and the aligned tip-label column, a small context menu offers Reset tip position, which restores the automatically calculated tip-label width.
To select or deselect a node without opening the menu, click on it. Hold a modifier and click to make an exclusive (single-node) selection.
Open the search bar from View → Find, the toolbar's magnifying-glass button, or the keyboard shortcut Cmd+F / Ctrl+F.
Type a query into the search box. TreeHouse performs a substring match across the tree's labels and updates the canvas immediately, highlighting all matching edges. The number of matches is reflected in the navigation buttons next to the search box:
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Left arrow / Right arrow: step through matches one at a time, scrolling the tree to bring each into view.
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Add to Selection: add every currently matched node to the selection.
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Remove from Selection: remove every currently matched node from the selection.
The ‘Tips Only’ checkbox restricts the search to leaf labels, which is useful when internal labels also contain text that would otherwise match.
The search bar can be hidden again with the same shortcut, the toolbar button, or the close action of the search input. Search state is preserved across sessions: if you reopen the search bar it remembers what you searched for.
When you have built up a selection by searching, turn on Selection Lock in the side bar to make it persistent against accidental clicks.
When the tree carries branch lengths and the Distance Unit is set to anything other than Unitless, you can open the Plot pane by clicking the Plot button in the tool bar.
Within the Plot pane:
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LTT (Lineages-Through-Time): toggle a Lineages-Through-Time curve aligned with the tree's time axis. When LTT is on, a Y-Axis Scale pick-list lets you choose between Linear, Log Base 2, and Log Base 10.
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Geological Time Scale: when the Distance Unit is Million years, this toggle paints the standard geological time scale across the plot's x-axis, making it easy to see which epochs and periods a node falls into.
The plot canvas is synchronized with the tree canvas: scrolling or resizing one updates the other.
Toggling the Node Table button in the tool bar shows a third pane below the tree containing a row for every node:
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Click any column header to sort by that field. Click again to reverse the sort order.
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Both the Node Table and an Attributes Table (when the tree carries node/branch attributes, e.g. from BEAST or annotated Newick) are sortable in the same way.
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Scrolling the table is independent of the tree canvas.
The table is a quick way to review tip names, branch lengths, and any associated attributes without scrolling the canvas itself.