Feature Reference
This section explains the controls and methods available after a dataset is loaded or prepared.
Use it when you need to answer practical questions such as:
- which setup settings affect tree inference,
- how branch-length and layout controls change the tree view,
- how to interpret the movie timeline and Transition Inspector,
- how MSA windows are synchronized with tree frames,
- how taxa coloring, subtree highlighting, and SPR analytics work,
- what the PNG and WebM export buttons save.
Most controls are context-sensitive. If a dataset does not include an MSA, branch annotations, generated transition frames, or SPR metadata, the matching controls are hidden, disabled, or report unavailable values.
Reference Pages
| Page | Covers |
|---|---|
| Setup and input | Upload modes, examples, backend availability, sliding windows, rooting, and inference settings. |
| Workspace controls | Sidebar groups, branch lengths, geometry, labels, layout, view mode, highlights, and focus effects. |
| Timeline and inspection | Playback, generated frames, comparison view, metrics chart, timeline hover, and Transition Inspector. |
| MSA viewer | Alignment window controls, region overrides, row ordering, color schemes, and synchronization. |
| Taxa coloring | Manual taxa colors, pattern grouping, CSV grouping, palettes, and reset actions. |
| SPR analytics | Moved-subtree overview, SPR move table, recurrent subtree table, branch support threshold, and CSV exports. |
| Export and recording | Canvas fit/zoom/reset, PNG export, WebM recording, and common export limitations. |