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@rivm-loculus-tools/phylogeny-viewer

v1.6.0

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florianzwagemakerflorianzwagemakeraximusaximus

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Readme

Phylogenetic Tree Viewer (loculus-tools/phylogeny-viewer)

A client-side interactive phylogenetic tree analysis tool and dedicated loculus-tool designed for rapid investigation and ad-hoc visualization of phylogenetic trees directly in the browser.

Features

  • Dual-Engine WASM Tree Calculation:
    • TN93 + Neighbor-Joining: Ultra-fast distance matrix computation converted via RapidNeighborJoining into Newick format.
    • FastTree (Biowasm): Neighbor-Joining (-noml -fastest) and Maximum Likelihood (ML) with customizable evolutionary models (GTR / Jukes-Cantor), bootstrapping iterations, and SPR rounds.
    • Parallel Dependency Preloader: Background preloading of fasttree/2.1.11 and tn93/1.0.11 via Web Workers (@biowasm/aioli).
  • Tree Visualization:
    • Rendered via @gen-epix/ui-casedb's PhylogeneticTreeComponent on high-DPI HTML5 Canvas.
    • Interactive mouse scroll zoom and click-and-drag panning with scale stability.
    • Distance scale bar with dynamic tick increments.
  • Pre-Alignment Sequence Validation:
    • Validates character length across FASTA headers. If unaligned sequences are provided, calculations are safely aborted and an informative warning modal is presented (INVALID_ALIGNMENT).
  • Metadata Enrichment & Color Mapping:
    • Deterministic palette generation for any TSV metadata attribute.
    • Interactive floating dynamic legend.
    • Composite leaf label builder (accessionVersion|Field1|Field2).
  • Interactivity & Inspection:
    • Real-time free-text search with prominent red outline highlights on matching leaf nodes.
    • Draggable inspection tooltips for leaf sample metadata and internal node clade collapse/expand.
  • Export Formats:
    • Save as Newick (.nwk), PNG image, JPEG image, and SVG vector format.
  • Deep Linking:
    • Auto-loads datasets on launch using ?input-fasta=<url> and ?input-metadata=<url> query parameters.

Getting Started

This package is part of the loculus-tools pnpm monorepo, so dependencies are installed from the repo root.

Development

pnpm install
pnpm --filter @rivm-loculus-tools/phylogeny-viewer start

Production Build

pnpm --filter @rivm-loculus-tools/phylogeny-viewer build
pnpm --filter @rivm-loculus-tools/phylogeny-viewer preview

Demo Data

Click Load Data -> Load Demo SARS-CoV-2 Data in the UI, or load:

  • FASTA: /sample-data/sarscov2_aligned.fasta
  • TSV: /sample-data/sarscov2_metadata.tsv