JLSteenwyk/orthosnap

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OrthoSNAP is a tree splitting and pruning tool for retrieving single-copy orthologous subgroups (SNAP-OGs) from larger gene families.

If you found OrthoSNAP useful, please cite:
OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees. Steenwyk et al. 2022, PLOS Biology. DOI: 10.1371/journal.pbio.3001827.

Full usage documentation and tutorial:
https://jlsteenwyk.com/orthosnap/

What's new in v1.6.0

Compared to v1.5.0 (plotting + performance improvements), v1.6.0 adds workflow-scale and reproducibility features:

• --manifest: batch execution from TSV/CSV manifests.
• --validate-only: preflight input concordance checks without extraction.
• --structured-output: machine-readable run metadata (.run.json) and subgroup summaries (.subgroups.tsv).
• --occupancy-count / --occupancy-fraction: explicit occupancy semantics.
• --resume: skip rerunning completed analyses.
• --bootstrap-trees + --consensus-min-frequency + --consensus-trees: consensus subgrouping across bootstrap tree uncertainty.

Compared to older releases:

• v1.5.0 focused on plotting and runtime optimization.
• v1.3.2 introduced configurable delimiters.
• v1.2.0 added inparalog handling reports.
• v1.0.0 and earlier focused on core pruning behavior.

Installation

Install with pip (recommended)

python -m venv .venv
source .venv/bin/activate
pip install orthosnap

Install from source

git clone https://github.com/JLSteenwyk/orthosnap.git
cd orthosnap
python -m venv .venv
source .venv/bin/activate
make install

Install with conda

conda install -c jlsteenwyk orthosnap

Conda package details:
https://anaconda.org/jlsteenwyk/orthosnap

Quick start

orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre

Generate a color-coded SNAP-OG assignment plot for the full tree:

orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre -ps

Choose plot format (png default, pdf or svg):

orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre -ps -pf svg

Show all CLI options:

orthosnap -h

Run validation checks only (no subgroup extraction):

orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre --validate-only

Write structured provenance outputs (.run.json and .subgroups.tsv):

orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre --structured-output

Resume an interrupted or previously completed run:

orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre --resume

Use explicit occupancy semantics:

orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre --occupancy-count 5
orthosnap -f orthogroup_of_genes.faa -t phylogeny_of_orthogroup_of_genes.tre --occupancy-fraction 0.5

Run many orthogroups from a manifest (TSV/CSV with tree and fasta columns):

orthosnap --manifest runs.tsv --structured-output -op results/

Run bootstrap consensus mode using a file of tree paths (one per line):

orthosnap -f orthogroup_of_genes.faa -t reference.treefile --bootstrap-trees bootstrap_paths.txt --consensus-min-frequency 0.5

Also write consensus Newick trees:

orthosnap -f orthogroup_of_genes.faa -t reference.treefile --bootstrap-trees bootstrap_paths.txt --consensus-trees

Support

If installation fails in a clean virtual environment, contact Jacob L. Steenwyk via:

• Email: https://jlsteenwyk.com/contact.html
• Twitter/X: https://twitter.com/jlsteenwyk