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02. Display options
A typical TreeHouse window has four major regions:
- Left side bar: controls for tree style, distance unit, node ordering, edge spacing, label visibility, label size, and other display settings.
- Tool bar: buttons for re-rooting, switching between trees (if your file contains more than one tree), viewing subtrees, opening the search bar, toggling the Plot pane, and toggling the Nodes Table.
- Center drawing canvas: the tree itself, drawn either as a phylogram (left-to-right rectangular tree) or a fan (circular tree).
- Right side bar: annotations, statistics, and other read-only information about the currently selected tree. Beneath these you can optionally show:
- Plot pane with a Lineages-Through-Time (LTT) plot and (where appropriate) a Geological Time Scale.
- Nodes Table that lists every node in the tree with sortable columns. Both of these extra panes share the central area; you can drag the divider to give them more or less space.
The left-hand side bar groups the most commonly used display options. Depending on the loaded tree, some controls may be hidden (for example, Distance Unit is only shown when the tree carries branch lengths).
At the top of the left side bar, you can find summary information pertaining to your tree. You should be able to see the number of tips and nodes, the height of the tree, and whether or not your tree is rooted, has branch lengths, and if it is ultrametric.
When a tree has branch lengths, you can tell TreeHouse what those lengths represent:
- Unitless: branch values are treated as opaque numbers. The plot pane and time-aware features are disabled.
- Subs. per site: substitutions per site (typical of molecular phylogenies estimated from sequence data).
- Million years: calibrated time. Choosing this unit reverses the x-axis so that time flows from past (left) to present (right), and unlocks the Geological Time Scale overlay.
- Coalescence: coalescent units (typical of population-genetic trees).
TreeHouse supports two layout styles:
- Phylogram: a left-to-right rectangular tree (the default). Best for medium-sized trees and for direct comparison of branch lengths.
- Fan: a circular tree. Best for very large trees or for a more compact overview. Node Ordering This pick-list reorders the children at every internal node for cleaner display:
- Unordered: leave the order as in the input file.
- Ascending (default): smaller subtrees on top.
- Descending: larger subtrees on top. Edge Spacing / Width / Zoom
These depend on the tree style.
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In Phylogram mode you can use the Edge Spacing slider (adjust vertical spacing between tips) and the Width slider (adjust horizontal spacing).
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In Fan mode you get a single Zoom slider, plus Opening Angle and Rotation sliders that control how much of the circle the tree occupies and how it is rotated. There is also a Root Length slider that adjusts how far the root edge extends to the left of (or in towards the center of) the tree.
- Root: draw or hide the root edge.
- Selection Lock: prevent further changes to the current selection. Useful when you have built up a selection by searching and want to avoid accidentally clearing it.
- Cursor Tracking Line (Phylogram) or Cursor Tracking Circle (Fan): a red vertical line guide will follow your cursor to make it easier to parse lengths across the tree.
- Scale Bar: show a scale bar along the bottom of the canvas. Full Width Scale Bar stretches it across the entire visible width. The default Scale Bar unit is millions of years, and the Full Width Scale Bar displays scale information from the root to the latest tip.
The right side bar contains toggles for controlling what is displayed on the tree (tip/node/branch labels). Options to format the labels become available when labels are toggled on.
Three independent toggles control which labels are drawn:
- Tip Labels: leaf names. On by default.
- Internal Labels: names assigned to internal nodes (for example, clade names or posterior support values stored as labels).
- Branch Lengths: numeric branch length values printed next to each branch.
For each of these, a separate slider sets the font size when toggled on. When Tip Labels is toggled, you can also:
- Align Tip Labels: draw the tip labels in a single column on the right edge of the tree, with dashed guide lines connecting each tip to its label.
- Trim Tip Labels: shorten long tip labels to a fixed character limit so they do not push the tree out of view; the cut-off length is itself adjustable with a slider.
The tool bar runs across the top of the drawing canvas. Tool bar buttons are displayed in dark blue when a user may perform the action and light blue when they are not available for use. From left to right it contains:
- Root: re-root the tree at a chosen node (use this together with the Root Here option in the right-click menu). Only one node should be selected (highlighted in yellow, with a red circular border) in order to use the Root option. If more than one node is selected, the Root option will not be available.
- Unroot: remove the current root and treat the tree as unrooted. The button is enabled only for rooted trees. If the tree is already rooted, the Unroot button will not remove the user selection for the rooted node. This means that the user’s last rooted node should be saved and used to Root the tree again even if the Unroot button has been pressed, reducing the time involved in manually rooting trees.
- Close Subtree: return to viewing the full tree.
Select a node and right click to open the subtree initially.
When a subtree view is active, the summary information in the left side bar shows tip and node counts as <subtree> / <full tree>, so you always know how many tips you are looking at relative to the whole tree.
If a file contains more than one tree (for example, a posterior or bootstrap sample), a switcher with previous and next arrows appears in the center of the tool bar. The numbers display the index of the current tree and the total number of trees in the file. Subtree viewing information is stored when switching between trees.
The right-hand group of buttons toggles three additional UI elements:
- Search: show or hide the search bar.
- Plot: show or hide the Plot pane below the tree (only enabled when the tree has branch lengths and a distance unit.
- Nodes Table: show or hide a sortable table of every node in the tree.