Command-line reference

The pipeline can be scripted instead of run through the UI. The core step is propose_sublineages.py (the AutoLin algorithm); it reads a UShER MAT and writes the proposed lineages. Run it in the image with the repo mounted:

docker run --rm -v "$PWD":/data -w /data ghcr.io/corbett-lab/linolium bash -lc '
  source /opt/conda/etc/profile.d/conda.sh && conda activate taxalin
  python /app/autolin/propose_sublineages.py -i tree.pb -o annotated.pb \
    -d proposed.tsv -l labels.tsv'

The app runs it with -m 10 -t 1 -u 0.95 -f 0 -d … -l … (plus -r when Recursive is on).

Options

Input / output

Flag	Description
-i, --input	UShER MAT protobuf to annotate (required)
-o, --output	Write the annotated protobuf here
-d, --dump	Write the proposed sublineages as a table
-l, --labels	Write lineage↔sample associations (formatted for matUtils annotate -c)
-v, --verbose	Print progress

Lineage criteria

Flag	Default	Description
-m, --minsamples	10	Minimum sample weight for a proposed lineage
-t, --distinction	1	Minimum mutations distinguishing a lineage from its parent
-u, --cutoff	0.95	Stop adding serial lineages once this fraction of samples is covered
-f, --floor	0	Minimum score to report a lineage
-r, --recursive	off	Recursively propose sublineages within proposals
-c, --clear	off	Clear existing annotations before starting

Scope

Flag	Description
-a, --annotation	Propose only within this lineage and its sublineages
-p, --samples	Restrict to samples in this file (sample weight per line)

Weighting and translation (advanced)

Flag	Description
-w, --mutweights	Per-mutation weights file (2–3 columns: mutation, weight, [node])
-y, --aaweights	Per-amino-acid-change weights; requires --gtf and --reference
-g, --gene	Consider only mutations in this gene; requires --gtf and --reference
-s, --missense	Consider only missense mutations; requires --gtf and --reference
--gtf	GTF for translation (use with --reference)
--reference	Reference FASTA for translation (use with --gtf)

Formats

Input — a UShER Mutation Annotated Tree protobuf (.pb or .pb.gz).

Outputs

File	Contents
-o protobuf	the tree with proposed auto.* lineages annotated
-d table	one row per proposed lineage (parent, node id, score, size)
-l table	sample-to-lineage assignments

The app additionally produces the Taxonium display file (.jsonl.gz), an annotated .pb.gz (re-uploadable for further curation), and a sample-to-lineage .tsv.