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https://github.com/jlsteenwyk/orthosnap
a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
https://github.com/jlsteenwyk/orthosnap
bioinformatics evolution evolutionary-biology genomics orthology orthology-assignments orthology-inference phylogenetics phylogenomics python
Last synced: 12 days ago
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a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
- Host: GitHub
- URL: https://github.com/jlsteenwyk/orthosnap
- Owner: JLSteenwyk
- License: mit
- Created: 2021-02-28T13:55:43.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2023-12-20T21:13:43.000Z (11 months ago)
- Last Synced: 2024-04-25T18:22:39.339Z (7 months ago)
- Topics: bioinformatics, evolution, evolutionary-biology, genomics, orthology, orthology-assignments, orthology-inference, phylogenetics, phylogenomics, python
- Language: Python
- Homepage: https://jlsteenwyk.com/orthosnap/
- Size: 112 MB
- Stars: 19
- Watchers: 4
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
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OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees.
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).
---
This documentation covers downloading and installing orthosnap. Details about orthosnap usage including a tutorial are available on our [online documentation](https://jlsteenwyk.com/orthosnap/).
**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
```
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*.**
To install via anaconda, execute the follwoing command:
``` shell
conda install -c jlsteenwyk orthosnap
```
Visit here for more information: https://anaconda.org/jlsteenwyk/orthosnap