Automated phylogenetic lineage proposal and interactive curation.

Linolium provides an environment for lineage discovery and curation on pathogen phylogenetic trees of virtually any size. It builds on the AutoLin algorithm for distance-based identification of clades and provides a UI for customizing the algorithm and curating results.

Use the web app:

➜ linolium.vercel.app

or run the Docker container locally for larger trees.

Quick Start (local)

docker run -it --memory=8g -v "$PWD":/data -p 3000:3000 ghcr.io/corbett-lab/linolium

Open http://localhost:3000, upload a .pb or .pb.gz file, and run the pipeline.

The app runs on a single port. If 3000 is taken on your machine, remap it — e.g. -p 8080:3000, then open http://localhost:8080.

How it works

AutoLin proposes sublineages, the tree is converted to Taxonium format, and the viewer displays it for curation. This runs either in server mode (the backend calls native tools — use this for very large trees) or entirely in the browser (the hosted site). See the architecture notes.

Contributing

See CONTRIBUTING.md. Licensed under GPL-3.0.

📖 See the Linolium documentation for detailed usage instructions.