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
  • The Developers
  • More Team Members
• Usage
  • Basic usage
  • 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
  • 1. Download test data
  • 2. Run OrthoSNAP
  • 3. Inspect output
  • Interpretation
• Change log
• Other software
  • ClipKIT
  • PhyKIT
  • orthofisher
  • treehouse
  • ggpubfigs
• FAQ