OrthoSNAP is a command-line 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. PLOS Biology. doi: 10.1371/journal.pbio.3001827.
Quick Start
1. Install with pip
We recommend using a virtual environment.
python -m venv .venv
source .venv/bin/activate
pip install orthosnap
Deactivate when finished:
deactivate
2. Install with conda
conda install -c jlsteenwyk orthosnap
More details: https://anaconda.org/JLSteenwyk/orthosnap
3. Install from source
git clone https://github.com/JLSteenwyk/orthosnap.git
cd orthosnap
python -m venv .venv
source .venv/bin/activate
make install
4. Show CLI help
orthosnap -h
- About
- Usage
- Version differences
- Basic usage
- Validation-only preflight
- Structured provenance outputs
- Occupancy modes
- Resume mode
- Batch manifest mode
- Bootstrap consensus mode
- Input requirements
- Accounting for tree uncertainty
- Choosing which inparalog to keep
- Inparalog handling report
- Specifying the delimiter
- Plotting SNAP-OG assignments
- Performance Benchmark
- All options
- Tutorial
- Change log
- Other software
- FAQ