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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.
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
# install
pip install phykit
# run
phykit <function> <input file>
Installation
If you are having trouble installing PhyKIT, please contact the lead developer, Jacob L. Steenwyk, via email or twitter 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:
# 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:
# deactivate virtual environment
deactivate
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/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:
# deactivate virtual environment
deactivate
Note, the virtual environment must be activated to use phykit.
To install via anaconda, execute the following command:
conda install bioconda::phykit
Visit here for more information: https://anaconda.org/bioconda/phykit
To test phykit installation, launch the help message
phykit -h
Release Maintenance
See the Bioconda automation guide for release-triggered recipe synchronization, credential setup, dry runs, and failure recovery.
1 maintainer
Metadata
1 maintainer
Release files for phykit 2.8.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| phykit-2.8.0.tar.gz | 645.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| phykit-2.8.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 1.4 MB
Release files / phykit-2.8.0.tar.gz
| Download URL | phykit-2.8.0.tar.gz |
|---|---|
| Size | 645.7 kB |
| Tags | Source |
|
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.11.14
|
Release files / phykit-2.8.0-py3-none-any.whl
| Download URL | phykit-2.8.0-py3-none-any.whl |
|---|---|
| Size | 735.7 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.11.14
|
