PhyloLens

PhyloLens is a VS Code extension focused on viewing phylogenetic trees across multiple common formats.

Disclaimer

This project was developed with significant assistance from a large language model (GPT-5 / Codex).

What It Does

• Adds an Open Tree Viewer button in the editor title for supported tree files.
• Adds Open Tree Viewer to Explorer right-click for supported tree files.
• Opens a dedicated tree viewer panel beside your text editor.
• Adds a keyboard shortcut: Ctrl+Alt+P (Cmd+Alt+P on macOS).
• Tree/source sync: click node/branch in viewer -> reveal source in editor.
• Tree/source sync: move cursor in editor -> highlight corresponding node in viewer.

Screenshots

Editor Discoverability

Where to find the Open Tree Viewer icon in the editor title area.

Main Viewer

Main viewer layout with title row, controls, and status badges.

Radial Layout

Radial layout variants and branch-length display.

Edit Actions

Tree edit actions (rooting, unrooting, swap, collapse).

Search And Export

Search workflow (Prev/Next/Clear) and image export controls.

Compact Menu Mode

Compact menu mode used on smaller screens.

Supported File Types

• .nwk
• .newick
• .tree
• .tre
• .treefile
• .nex
• .nexus
• .phyloxml
• .xml (PhyloXML content)
• .nexml

Viewer Features

• Layouts: Rectangular (lengths), Rectangular (equal), Radial (lengths, curved), Radial (lengths, straight), Radial (equal, curved), Radial (equal, straight).
• Zoom and pan with +, -, mouse wheel, and drag.
• Fit view control (centers/fits tree with overlays visible).
• Scale indicator badge + optional scale bar in-canvas.
• Display toggles include branch lengths, scale bar, tip/internal labels, and node shapes.
• Selection-aware actions: root on selected branch, unroot, swap selected node child order, collapse/expand selected clade.
• Global undo (Ctrl+Z / Cmd+Z) for tree edits and view changes, plus revert-to-original.
• Save edited tree via Save As... format dropdown in Newick/NEXUS/PhyloXML/NeXML.
• Export rendered tree to SVG or PNG.
• Search taxon/node labels with Prev/Next, Clear, and a match counter.
• Branch hover details (length and descendant tip count).
• Rooted layouts render a short ancestral stem at the root.
• Large-tree guardrails:
  • auto-disable expensive overlays for large trees
  • auto-collapse very large trees to an overview
  • optional Safe mode prompt for extremely large trees

Metadata Badges

Title row badges show:

• source format
• edit sync status vs loaded source file

Bottom status strip badges show:

• rooted/unrooted
• bifurcating/non-bifurcating
• ultrametric/not ultrametric
• scale value
• performance (parse/render timing)

Install / Run (Dev)

npm install
npm run compile

Press F5 in VS Code to launch the Extension Development Host.

Changelog

• See CHANGELOG.md for release history and notable changes.

Example Trees

All example trees now live under examples/.

Small/base examples:

• examples/comments.nwk
• examples/sample.nexml
• examples/sample.nexus
• examples/sample.nwk
• examples/sample.phyloxml
• examples/sample.rooted.nwk
• examples/polytomy.rooted.nwk
• examples/polytomy.unrooted.nwk
• examples/polytomy.unrooted.internal.nwk
• examples/polytomy.sample.nexus
• examples/ultrametric.nwk

Polytomy note:

• In unrooted mode, the required 3-way display root is not treated as a polytomy.
• examples/polytomy.unrooted.nwk shows a top-level unrooted polytomy.
• examples/polytomy.unrooted.internal.nwk shows a clearly internal unrooted polytomy.

Rich metadata examples:

• examples/rich.nexml
• examples/rich.nexus
• examples/rich.phyloxml

Large examples:

• examples/large.nexml
• examples/large.nexus
• examples/large.nwk
• examples/large.phyloxml