Lineage Curation

Automated phylogenetic lineage proposal and interactive curation.

Input: UShER MAT protobuf file (.pb)
Output: Proposed sub-lineages + interactive curation UI

Build the Docker Container

# Build once
docker build -t lineage-curation .

Run Autolin

# Interactive mode with ports exposed
docker run -it -v "$PWD":/workspace -p 3000:3000 -p 8001:8001 lineage-curation

# Inside container - generate lineage proposals for an input UShER tree, create output tree with proposed lineage annotations
cd /workspace/autolin
python propose_sublineages.py -i /workspace/<input_tree>.pb -o /workspace/<tree_with_lineages>.pb

# Convert Autolin output tree to Taxonium format. Creates <tree_with_lineages>.jsonl.gz file in same directory as <tree_with_lineages>.pb
python convert_autolinpb_totax.py -a /workspace/<tree_with_lineages>.pb

Run Lineage Curation UI

cd /workspace/ui/linolium
./run-prod.sh /workspace/<tree_with_lineages>.jsonl.gz # Starts frontend web UI on port 3000, backend on 8001

View and edit lineages in UI

Open http://localhost:3000 in a web browser

Components

• autolin/ - Autolin algorithm for lineage proposals
• ui/ - Web interface for curation
• recombination-detection/ - Recombination analysis