A modern, browser-based phylogenetic tree viewer — the successor to FigTree
Browser app · Desktop download · Manual · Source code
PearTree is a phylogenetic tree viewer that runs entirely in your browser or as a native desktop application (macOS, Windows, Linux). It is the direct successor to FigTree and is designed to replace it for the everyday tasks of exploring, annotating, and publishing phylogenetic trees — including the large, richly annotated trees produced by BEAST and BEAST X.
No data is ever uploaded to a server. All processing runs locally on your machine.
- Reads NEXUS and Newick files, including full support for BEAST/BEAST X metacomment annotations (HPD intervals, posterior values, node heights, etc.)
- Smooth pan and zoom with mouse or trackpad; animated fit-to-window and fit-labels modes
- Hyperbolic lens — magnify any part of a large tree without losing context
- Subtree navigation — drill into any clade and climb back up through a navigation history
- Node bars — display HPD intervals or range whiskers on internal nodes (BEAST output)
- Branch ordering — sort clades ascending or descending by clade size
- Rotation — flip individual nodes or entire subtrees
- Collapse / expand — collapse clades to triangles with configurable height and labels
- Hide / show — hide entire subtrees while retaining tree topology
- Import metadata from CSV / TSV files and join on tip names
- Colour tips, nodes, branches, and labels by any annotation — categorical or continuous
- Multiple configurable legend panels with palette and scale-mode overrides
- Annotation Curator — rename, reorder, delete, and edit annotation values in-app
- Data Table panel — spreadsheet-like view of tip annotations, aligned with the tree; supports inline editing
- Full support for BEAST continuous and discrete trait annotations
- Midpoint rooting — find the root at the midpoint of the longest path
- Temporal rooting — global or branch-local root search maximising clock-signal R²
- Root-to-tip (RTT) panel — interactive regression plot; click points to select tips; export RTT data as CSV
- Calibrated time axis — map divergence to calendar dates using any date annotation
- Click tips or nodes; extend selections with Shift-click or drag; select-all
- Tip filter box — filter by any annotation with field / operator / value selectors
- Saved filters — store and restore named filter sets
- Highlight and paint (user-assigned colours) selected clades
- Themes — built-in Solarized dark/light palettes; save custom themes; set a default
- Light/dark mode toggle
- Export trees as NEXUS or Newick, optionally embedding PearTree display settings
- Export graphics as SVG or PNG at any resolution; export RTT plot as SVG/PNG
- Embed display settings in NEXUS files so collaborators see the same view on open
- Natively parses all BEAST 1 and BEAST X NEXUS output formats
- Displays node bars (HPD intervals) aligned with internal nodes
- First-class support for
height,height_95%_HPD,height_median,posterior,rate, and all standard BEAST annotations out of the box - Temporal rooting and RTT analysis designed for clock-calibrated phylogenies
- Web application at peartree.live — works in any modern browser with no installation
- Desktop app (via Tauri 2) for macOS, Windows, and Linux — native file open/save dialogs, file-type associations, and auto-updates
- Open remote tree files by URL; share links that pre-load a specific tree (
?treeUrl=…)
| Platform | Link |
|---|---|
| Web app (no install) | https://peartree.live |
| macOS (Apple Silicon & Intel) | GitHub Releases |
| Windows | GitHub Releases |
| Linux | GitHub Releases |
| Main view | Visual Options palette |
|---|---|
| Screenshot coming soon | Screenshot coming soon |
| Root-to-Tip panel | Data Table panel |
|---|---|
| Screenshot coming soon | Screenshot coming soon |
- Manual: https://artic-network.github.io/peartree/manual/
- Embedding API: embedded-api.md — embed PearTree in your own web pages
- URL/UI/Settings reference: url-settings-reference.md — complete query params plus
uiandsettingskeys - Settings object reference: settings-object-reference.md — complete settings key table with allowed values and defaults
- Tauri build notes: tauri-build.md
Design & development: Andrew Rambaut (University of Edinburgh)
Coding: Claude Sonnet 4.6 within GitHub Copilot & Andrew Rambaut
Development of PearTree has been supported by:
-
Wellcome Trust — through the ARTIC Network, a project developing rapid genomic surveillance and outbreak response tools for viral pathogens (Discretionary Award 313694/Z/24/Z and Collaborative Award 206298/Z/17/Z).
-
Gates Foundation — supporting open-source genomic epidemiology tools for global health.
The ARTIC Network is a collaborative project focused on real-time genomic surveillance of viral outbreaks. It develops open laboratory protocols, bioinformatics pipelines, and analysis tools — including PearTree — to enable rapid phylogenetic analysis during public health emergencies. ARTIC tools have been deployed in responses to Ebola, SARS-CoV-2, and other viral outbreaks worldwide.
PearTree is open source and released under the MIT License.
Source code: github.com/artic-network/peartree
Web / UI
- PearCore — Common ARTIC App Framework
- Bootstrap 5 — UI framework
- Bootswatch Solar — dark theme
- Bootstrap Icons — iconography
- Marked — Markdown rendering
Desktop app
- Tauri 2 — cross-platform desktop shell (Rust + WebView)
- tauri-plugin-dialog — native file open/save dialogs
- tauri-plugin-opener — open URLs and files in system default apps
- tauri-plugin-deep-link — file-association and URL-scheme handling
- tauri-plugin-updater — automatic update delivery
- serde — Rust serialisation framework
- base64 — base64 encoding/decoding