OrthoSNAP is a command-line tool for increasing the size of molecular evolution datasets that can then be used for diverse studies including phylogenomics and genome-wide surveys of positive selection.

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) Installation

To install using pip, we strongly recommend building a virtual environment to avoid software dependency issues. To do so, execute the following commands:

# create virtual environment
python -m venv .venv
# activate virtual environment
source .venv/bin/activate
# install orthosnap
pip install orthosnap

Note, the virtual environment must be activated to use OrthoSNAP.

After using OrthoSNAP, you may wish to deactivate your virtual environment and can do so using the following command:

# deactivate virtual environment
deactivate

To install via anaconda, execute the following command:

conda install -c jlsteenwyk orthosnap

Visit here for more information: https://anaconda.org/JLSteenwyk/orthosnap

Similarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands:

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

To deactivate your virtual environment, use the following command:

# deactivate virtual environment
deactivate

Note, the virtual environment must be activated to use orthosnap.

2) Usage

Get the help message from orthosnap:

orthosnap -h