PearTree is a fast, interactive phylogenetic tree viewer designed for genomic epidemiology. It can display large NEXUS and Newick trees with rich visual controls, colour branches and tips by any annotation, show a time-calibrated axis, and export publication-quality SVG or PNG figures.
Using PearTree
Web app
The easiest way to use PearTree is directly in your browser — no installation required:
https://artic-network.github.io/peartree
Drag and drop a NEXUS or Newick tree file onto the canvas, or use the Open… button. You can also load example data or point the app at a tree file URL.
Desktop app
A native desktop application is available for macOS, Windows, and Linux, built with Tauri. It offers the same features as the web app with native file system access and the ability to open FASTA files directly from your file manager.
Pre-built installers for the latest release can be downloaded from the GitHub Releases page:
| Platform | Installer |
|---|---|
| macOS — Apple Silicon (M1/M2/M3/M4) | PearTree_x.x.x_aarch64.dmg |
| macOS — Intel (x86-64) | PearTree_x.x.x_x64.dmg |
| Windows | PearTree_x.x.x_x64-setup.exe |
| Linux (Debian/Ubuntu) | peartree_x.x.x_amd64.deb |
| Linux (AppImage) | peartree_x.x.x_amd64.AppImage |
Key features
- Annotation colouring — colour tip labels, tip shapes, and internal nodes by any annotation field loaded from the tree or imported from a CSV/TSV file; categorical and continuous colour palettes supported
- Hyperbolic lens — expand a region of a large tree to label-readable spacing without losing sight of the rest
- Subtree navigation — double-click any node to drill down into its clade; navigate back and forward through your view history
- Time-calibrated axis — calibrate using a date annotation, then display a calendar-date axis with configurable major/minor tick intervals
- Import annotations — load per-tip metadata from a CSV or TSV file and map it to any annotation field in the tree
- Hide/show subtrees — remove nodes and clades from the view to focus on subsets of interest
- Branch ordering and rotation — sort clades by size ascending or descending, or rotate individual nodes
- Export tree — save as NEXUS (with embedded visual settings) or Newick; choose entire tree or current subtree view
- Export graphic — export the current view or full tree as SVG (vector) or PNG (2× raster)
- BEAST tree support — displays node height HPD bars and recognises posterior probability and other annotations from BEAST output
Source code & issues
PearTree is open-source software. Source code and issue tracker are on GitHub: https://github.com/artic-network/peartree