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: about 2 months 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 (almost 4 years ago)
• Default Branch: master
• Last Pushed: 2023-12-20T21:13:43.000Z (about 1 year ago)
• Last Synced: 2024-04-25T18:22:39.339Z (8 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