PURPOSE

Bring broadscale comparative genomics to the masses. Taxonomy-agnostic, with automated data acquisition operational with prokaryote, animal, plant, and fungal genome data.

Mycotools is a compilation of computational biology tools and database (MycotoolsDB/MTDB) software that facilitate large-scale comparative genomics. MycotoolsDB dereplicates and locally assimilates NCBI and MycoCosm (Joint Genome Institute) genomes into a database schema with uniform file curation, scalability, and automation as guiding principles.

  • Database initialization: mtdb u --init <DIR>
  • Database updating: mtdb u --update
  • The MycotoolsDB (MTDB) uniformly curates GenBank/MycoCosm and local gff formats into a consistent standard
  • The .mtdb database format is a uniform input for analyses with 100,000s to as few as a single genome
  • Mycotools software suite includes modules to automate routine-complex comparative genomics, such as phylogenetic analysis


INSTALL

Please review the wiki for installation and usage information!


CITING

If Mycotools contribute to your analysis, please cite the preprint and mention the version in-line.

Konkel, Z., Slot, J. C. Mycotools: An Automated and Scalable Platform for Comparative Genomics. bioRxiv 2023.09.08.556886; doi: https://doi.org/10.1101/2023.09.08.556886

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

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

Credits

Author: Zachary Konkel

License

GNU Lesser General Public License v3 or later (LGPLv3+) (Copyright 2023 Zachary Konkel)

Requires

Python <4, >=3.0

Classifiers

Report project as malware

Metadata

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

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

Credits

Author: Zachary Konkel

License

GNU Lesser General Public License v3 or later (LGPLv3+) (Copyright 2023 Zachary Konkel)

Requires

Python <4, >=3.0

Classifiers

Report project as malware

Release files for mycotools 1.0.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for mycotools 1.0.0
File Size Uploaded
mycotools-1.0.0.tar.gz 1.9 MB Details

Built distribution (wheel)

Table of built distributions (wheels) for mycotools 1.0.0
File Interpreter ABI Platform
mycotools-1.0.0-py3-none-any.whl 214.7 kB Python 3 none any Details

Total release size: 2.1 MB

Release files / mycotools-1.0.0.tar.gz

Download URL mycotools-1.0.0.tar.gz
Size 1.9 MB
Tags Source
SHA-256 checksum
How to use checksums 		6dbe0f25655da6e27e26166858703550bd46a86c2f8d04afe5b047dfbe0337da
BLAKE2b-256 checksum
How to use checksums 		2e46575c6f9abf6e5b409d7a9b7a581fe128db7d7bddbdc49c3678e310c736e1
Upload date
Uploaded using Trusted Publishing?
What is trusted publishing? 		No
Uploaded via twine/6.1.0 CPython/3.9.21

Release files / mycotools-1.0.0-py3-none-any.whl

Download URL mycotools-1.0.0-py3-none-any.whl
Size 214.7 kB
Tags Python 3
SHA-256 checksum
How to use checksums 		9165bda9a5eb709844ad212a25136e0f2d814ea1586ec2f31e4eb48567c24da7
BLAKE2b-256 checksum
How to use checksums 		7e75744ed2deebf59888383b323ea9a90756c8e69ea769700d9a038ca8655897
Upload date
Uploaded using Trusted Publishing?
What is trusted publishing? 		No
Uploaded via twine/6.1.0 CPython/3.9.21

Release history Release notifications | RSS feed

This release

1.0.0 This release

2 release files

0.32.11

1 release file

0.32.10

2 release files

0.32.9

2 release files

0.32.8

2 release files

0.32.7

2 release files

0.32.6

2 release files

0.32.5

2 release files

0.32.4

2 release files

0.32.3

2 release files

0.32.2

1 release file

0.32.1

2 release files

0.31.49

2 release files

0.31.48

1 release file

0.31.47

2 release files

0.31.46

2 release files

0.31.45

2 release files

0.31.44

2 release files

0.31.43

2 release files

0.31.42

2 release files

0.31.41

2 release files

0.31.40

2 release files

0.31.39

2 release files

0.31.38

2 release files

0.31.37

2 release files

0.31.36

2 release files

0.31.35

2 release files

0.31.34

2 release files

0.31.33

2 release files

0.31.32

2 release files

0.31.31

2 release files

0.31.30

2 release files

0.31.29

2 release files

0.31.28

2 release files

0.31.27

2 release files

0.31.26

2 release files

0.31.25

2 release files

0.31.24

2 release files

0.31.23

2 release files

0.31.22

2 release files

0.31.21

2 release files

0.31.20

2 release files

0.31.19

2 release files

0.31.18

2 release files

0.31.17

2 release files

0.31.16

2 release files

0.31.15

2 release files

0.31.14

2 release files

0.31.13

2 release files

0.31.12

2 release files

0.31.11

2 release files

0.31.10

2 release files

0.31.9

2 release files

0.31.8

2 release files

0.31.7

2 release files

0.31.6

2 release files

0.31.5

2 release files

0.31.4

2 release files

0.31.3

2 release files

0.31.2

2 release files

0.31.1

2 release files

0.31.0

2 release files

0.30.95

2 release files

0.30.94

2 release files

0.30.93

2 release files

0.30.91

2 release files

0.30.90

2 release files

0.30.89

2 release files

0.30.88

2 release files

0.30.87

2 release files

0.30.86

2 release files

0.30.85

2 release files

0.30.84

2 release files

0.30.83

2 release files

0.30.82

2 release files

0.30.81

2 release files

0.30.80

2 release files

0.30.79

2 release files

0.30.78

2 release files

0.30.77

2 release files

0.30.76

2 release files

0.30.75

2 release files

0.30.74

2 release files

0.30.73

2 release files

0.30.72

2 release files

0.30.71

2 release files

0.30.70

2 release files

0.30.69

2 release files

0.30.68

2 release files

0.30.67

2 release files

0.30.66

2 release files

0.30.65

2 release files

0.30.64

2 release files

0.30.63

2 release files

0.30.62

2 release files

0.30.61

2 release files

0.30.60

2 release files

0.30.59

2 release files

0.30.58

2 release files

0.30.57

2 release files

0.30.56

2 release files

0.30.55

2 release files

0.30.54

2 release files

0.30.53

2 release files

0.30.52

2 release files

0.30.51

2 release files

0.30.50

2 release files

0.30.49

2 release files

0.30.48

2 release files

0.30.47

2 release files

0.30.46

2 release files

0.30.45

2 release files

0.30.44

1 release file

0.30.43

2 release files

0.30.42

2 release files

0.30.41

2 release files

0.30.40

2 release files

0.30.39

2 release files

0.30.38

2 release files

0.30.37

2 release files

0.30.36

2 release files

0.30.35

2 release files

0.30.33

2 release files

0.30.32

2 release files

0.30.31

2 release files

0.30.30

2 release files

0.30.29

2 release files

0.30.28

2 release files

0.30.27

2 release files

0.30.26

2 release files

0.30.25

2 release files

0.30.24

2 release files

0.30.23

2 release files

0.30.22

2 release files

0.30.21

2 release files

0.30.20

2 release files

0.30.18

2 release files

0.30.17

2 release files

0.30.16

2 release files

0.30.15

2 release files

0.30.14

2 release files

0.30.13

2 release files

0.30.12

2 release files

0.30.11

2 release files

0.30.10

2 release files

0.30.9

2 release files

0.30.7

2 release files

0.30.6

2 release files

0.30.5

2 release files

0.30.4

2 release files

0.30.3

2 release files

0.30.2

2 release files

0.30.1

2 release files

0.27.36

2 release files

0.27.35

2 release files

0.27.34

2 release files

0.27.33

2 release files

0.27.32

2 release files

0.27.31

2 release files

0.27.30

2 release files

0.27.29

2 release files

0.27.28

2 release files

0.27.27

2 release files

0.27.26

2 release files

0.27.25

2 release files

0.27.24

2 release files

0.27.23

2 release files

0.27.22

2 release files

0.27.21

2 release files

0.27.20

2 release files

0.27.19

2 release files

0.27.18

2 release files

0.27.17

2 release files

0.27.16

2 release files

0.27.15

2 release files

0.27.14

2 release files

0.27.13

2 release files

0.27.12

2 release files

0.27.11

2 release files

0.27.10

2 release files

0.27.9

2 release files

0.27.8

2 release files

0.27.7

2 release files

0.27.6

2 release files

0.27.5

2 release files

0.27.4

2 release files

0.27.3

2 release files

0.27.2

2 release files

0.26.45

2 release files

0.26.44

2 release files

0.26.43

2 release files

0.26.42

2 release files

0.26.41

2 release files

0.26.40

2 release files

0.26.39

2 release files

0.26.38

2 release files

0.26.37

2 release files

0.26.36

2 release files

0.26.35

2 release files

0.26.34

2 release files

0.26.33

2 release files

0.26.32

2 release files

0.26.31

2 release files

0.26.30

2 release files

0.26.29

2 release files

0.26.28

2 release files

0.26.27

2 release files

0.26.26

2 release files

0.26.25

2 release files

0.26.24

2 release files

0.26.23

2 release files

0.26.22

2 release files

0.26.21

2 release files

0.26.19

1 release file

0.26.18

2 release files

0.26.17

2 release files

0.26.14

2 release files

0.26.13

2 release files

0.26.12

2 release files

0.26.11

2 release files

0.26.10

2 release files

0.26.9

2 release files

0.26.8

2 release files

0.26.7

2 release files

0.26.5

2 release files

0.26.4

2 release files

0.26.3

2 release files

0.26.2

2 release files

0.26.1

2 release files

0.26

2 release files

0.25

2 release files

0.24

2 release files

0.23

2 release files

0.22

2 release files

0.21

2 release files

0.20

2 release files

0.19

2 release files

0.18

2 release files

0.16

2 release files

0.15

2 release files

Pre-release

0.15b1

2 release files

0.14

2 release files

0.13

2 release files

0.12

2 release files

Pre-release

0.11b24

2 release files

Pre-release

0.11b23

2 release files

Pre-release

0.11b22

2 release files

Pre-release

0.11b21

2 release files

Pre-release

0.11b20

2 release files

Pre-release

0.11b19

2 release files

Pre-release

0.11b18

2 release files

Pre-release

0.11b17

2 release files

Pre-release

0.11b16

2 release files

Pre-release

0.11b15

2 release files

Pre-release

0.11b14

2 release files

Pre-release

0.11b12

2 release files

Pre-release

0.11b11

2 release files

Pre-release

0.11b10

2 release files

Pre-release

0.11b9

2 release files

Pre-release

0.11b6

2 release files

Pre-release

0.11b5

2 release files

Pre-release

0.11b4

2 release files

Pre-release

0.11b2

2 release files

Pre-release

0.11b1

2 release files

Pre-release

0.10b12

2 release files

Pre-release

0.10b11

2 release files

Pre-release

0.10b10

2 release files

Pre-release

0.10b9

2 release files

Pre-release

0.10b8

2 release files

Pre-release

0.10b7

2 release files

Pre-release

0.10b6

2 release files

Pre-release

0.10b5

2 release files

Pre-release

0.10b4

2 release files

Pre-release

0.10b3

2 release files

Pre-release

0.10b2

2 release files

Pre-release

0.10b1

2 release files

Pre-release

0.9b37

2 release files

Pre-release

0.9b36

2 release files

Pre-release

0.9b35

2 release files

Pre-release

0.9b34

2 release files

Pre-release

0.9b33

2 release files

Pre-release

0.9b32

2 release files

Pre-release

0.9b31

2 release files

Pre-release

0.9b30

2 release files

Pre-release

0.9b29

2 release files

Pre-release

0.9b28

2 release files

Pre-release

0.9b27

2 release files

Pre-release

0.9b26

2 release files

Pre-release

0.9b25

2 release files

Pre-release

0.9b24

2 release files

Pre-release

0.9b23

2 release files

Pre-release

0.9b22

1 release file

Pre-release

0.9b21

2 release files

Pre-release

0.9b20

2 release files

Pre-release

0.9b19

2 release files

Pre-release

0.9b18

2 release files

Pre-release

0.9b17

2 release files

Pre-release

0.9b16

2 release files

Pre-release

0.9b15

2 release files

Pre-release

0.9b14

2 release files

Pre-release

0.9b13

2 release files

Pre-release

0.9b12

2 release files

Pre-release

0.9b10

2 release files

Pre-release

0.9b9

2 release files

Pre-release

0.9b8

2 release files

Pre-release

0.9b7

2 release files

Pre-release

0.9b6

2 release files

Pre-release

0.9b5

2 release files

Pre-release

0.9b4

2 release files

Pre-release

0.9b3

2 release files

Pre-release

0.9b2

2 release files

Pre-release

0.9b1

2 release files

0.5.25

2 release files

0.5.23

2 release files

0.5.22

2 release files

0.5.20

2 release files

0.5.19

2 release files

0.5.18

2 release files

0.5.17

2 release files

0.5.15

2 release files

0.5.14

2 release files

0.5.13

2 release files

0.5.12

2 release files

0.5.11

2 release files

0.5.10

2 release files

0.5.9

2 release files

0.5.8

1 release file

0.5.7

1 release file

0.5.6

1 release file

0.5.5

1 release file

0.5.4

1 release file

0.5.3

1 release file

0.5.1

2 release files

Pre-release

0.5.1b1

1 release file

Pre-release

0.5.1b0

1 release file

Pre-release

0.5.0b0

1 release file

Anthropic, PBC Visionary sponsor Bloomberg Visionary sponsor Hudson River Trading Visionary sponsor Meta Visionary sponsor NVIDIA Visionary sponsor Microsoft Sustainability sponsor Depot Continuous Integration AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Sentry Error logging StatusPage Status page