Logo

Docs · Report Bug · Request Feature


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

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (2.6.0)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for JLSteenwyk from gravatar.com JLSteenwyk

Credits

Author: Jacob L. Steenwyk

Requires

Python >=3.10

Classifiers

Report project as malware

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

phykit-2.5.0.tar.gz (622.4 kB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

phykit-2.5.0-py3-none-any.whl (710.9 kB view details)

Uploaded Python 3

File details

Details for the file phykit-2.5.0.tar.gz.

File metadata

  • Download URL: phykit-2.5.0.tar.gz
  • Upload date:
  • Size: 622.4 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.2.0 CPython/3.11.14

File hashes

Hashes for phykit-2.5.0.tar.gz
Algorithm Hash digest
SHA256 bfa82f9ec684ffa4f123a6e9a67ee202db32bab1c4ecf65b9a7127d4c50bf767
MD5 bc6fce0c326c943a3231e261139af1ea
BLAKE2b-256 94ccef81bbe5f49c74116050600e3d3e5342e081a42a749e16956a1debe17c46

See more details on using hashes here.

File details

Details for the file phykit-2.5.0-py3-none-any.whl.

File metadata

  • Download URL: phykit-2.5.0-py3-none-any.whl
  • Upload date:
  • Size: 710.9 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.2.0 CPython/3.11.14

File hashes

Hashes for phykit-2.5.0-py3-none-any.whl
Algorithm Hash digest
SHA256 5e232b321f48c5fdd8507e301e69073f0c0397d6b39086802a96ccd03d0cd4ee
MD5 5e34e2225e5894f15811cf0deb5c122c
BLAKE2b-256 bfadfcd5eb677234f579d59dad4729686ac2c201a05999f544d104d5a2582f30

See more details on using hashes here.

Release history Release notifications | RSS feed

2.6.0

This release

2.5.0

2.4.1

2.4.0

2.3.0

2.2.1

2.2.0

2.1.94

2.1.93

2.1.92

2.1.90

2.1.89

2.1.88

2.1.87

2.1.85

2.1.84

2.1.83

2.1.82

2.1.81

2.1.80

2.1.79

2.1.78

2.1.76

2.1.75

2.1.74

2.1.73

2.1.72

2.1.71

2.1.70

2.1.69

2.1.68

2.1.67

2.1.66

2.1.64

2.1.63

2.1.62

2.1.61

2.1.60

2.1.59

2.1.57

2.1.56

2.1.55

2.1.54

2.1.52

2.1.51

2.1.50

2.1.49

2.1.48

2.1.47

2.1.46

2.1.45

2.1.44

2.1.43

2.1.42

2.1.41

2.1.40

2.1.39

2.1.38

2.1.37

2.1.35

2.1.34

2.1.33

2.1.32

2.1.31

2.1.30

2.1.28

2.1.27

2.1.26

2.1.25

2.1.23

2.1.21

2.1.20

2.1.16

2.1.12

2.1.11

2.1.10

2.1.8

2.1.5

2.1.4

2.1.2

2.1.1

2.1.0

2.0.3

2.0.2

2.0.1

2.0.0

1.20.0

1.19.9

1.19.8

1.19.7

1.19.6

1.19.5

1.19.4

1.19.3

1.19.2

1.19.1

1.19.0

1.17.0

1.16.0

1.14.0

1.13.1

1.13.0

1.12.6

1.12.5

1.12.4

1.12.3

1.12.2

1.12.0

1.11.16

1.11.15

1.11.14

1.11.13

1.11.12

1.11.10

1.11.9

1.11.7

1.11.6

1.11.5

1.11.3

1.11.2

1.11.1

1.11.0

1.10.1

1.10.0

1.9.0

1.8.0

1.7.0

1.6.0

1.5.1

1.5.0

1.4.2

1.4.1

1.3.0

1.2.3

1.2.2

1.2.1

1.2.0

1.1.3

1.1.2

1.1.1

1.0.3

1.0.2

1.0.1

1.0.0

0.1.3

0.1.2

0.1.1

0.1.0

0.0.9

0.0.8

0.0.7

0.0.6

0.0.5

0.0.4

0.0.3

0.0.2

0.0.1

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Sentry Error logging StatusPage Status page