https://github.com/jlsteenwyk/phykit

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
https://github.com/jlsteenwyk/phykit

bioinformatics evolution evolutionary-biology genomics multiple-sequence-alignments phylogenetics phylogenomics python

Last synced: 2 days ago
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a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

• Host: GitHub
• URL: https://github.com/jlsteenwyk/phykit
• Owner: JLSteenwyk
• License: mit
• Created: 2020-05-12T14:29:24.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2024-09-19T22:34:01.000Z (3 months ago)
• Last Synced: 2024-10-18T14:55:24.734Z (2 months ago)
• Topics: bioinformatics, evolution, evolutionary-biology, genomics, multiple-sequence-alignments, phylogenetics, phylogenomics, python
• Language: Python
• Homepage: https://jlsteenwyk.com/PhyKIT/
• Size: 17.5 MB
• Stars: 58
• Watchers: 5
• Forks: 7
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • Changelog: change_log.txt
  • License: LICENSE.md

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PhyKIT is a UNIX shell toolkit for processing and analyzing phylogenomic data.



If you found PhyKIT useful, please cite *PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data*. Bioinformatics. doi: [10.1093/bioinformatics/btab096](https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btab096/6131675).





---

This documentation covers downloading and installing PhyKIT. Details about each function as well as tutorials for using PhyKIT are available in the online documentation.




**Quick Start**

```shell

# install

pip install phykit

# run

phykit  

```




**Installation** 


**If you are having trouble installing PhyKIT, 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 phykit

pip install phykit

```

**Note, the virtual environment must be activated to use phykit.**

After using PhyKIT, 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/PhyKIT.git

cd PhyKIT/

# 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 phykit.**




To install via anaconda, execute the following command:

```shell

conda install bioconda::phykit

```

Visit here for more information:

https://anaconda.org/bioconda/phykit




To test phykit installation, launch the help message

```shell

phykit -h

```