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OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees.<br /><br />
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](https://jlsteenwyk.com/publication_pdfs/2022_Steenwyk_etal_PLoS_Biology.pdf).
<br /><br />
---
<br />
This documentation covers downloading and installing orthosnap. Details about orthosnap usage including a tutorial are available on our [online documentation](https://jlsteenwyk.com/orthosnap/).
<br />
**Installation**
**If you are having trouble installing orthosnap, please contact the lead developer, Jacob L. Steenwyk, via [email](https://jlsteenwyk.com/contact.html) or [twitter](https://twitter.com/jlsteenwyk) to get help.**
To install using *pip*, we strongly recommend building a virtual environment to avoid software dependency issues. To do so, execute the following commands:
```shell
# 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:
```shell
# deactivate virtual environment
deactivate
```
<br />
Similarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands:
```shell
# 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:
```shell
# deactivate virtual environment
deactivate
```
**Note, the virtual environment must be activated to use *orthosnap*.**
<br />
To install via anaconda, execute the follwoing command:
``` shell
conda install -c jlsteenwyk orthosnap
```
Visit here for more information: https://anaconda.org/jlsteenwyk/orthosnap
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