orthosnap 1.5.0

orthosnap, identify orthologous subgroups of genes in large orthologous groups of genes.

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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.

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

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

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