clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

https://github.com/jlsteenwyk/clipkit

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 3 DOI reference(s) in README
✓
Academic publication links
Links to: plos.org, zenodo.org
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.3%) to scientific vocabulary

Keywords

bioinformatics evolution evolutionary-biology genomics phylogenetics phylogenomics python systematics

Keywords from Contributors

interactive serializer packaging network-simulation shellcodes hacking autograding observability embedded optim

Last synced: 6 months ago · JSON representation

Repository

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

Basic Info

Host: GitHub
Owner: JLSteenwyk
License: mit
Language: Python
Default Branch: master
Homepage: https://jlsteenwyk.com/ClipKIT/
Size: 25.9 MB

Statistics

Stars: 77
Watchers: 7
Forks: 5
Open Issues: 10
Releases: 14

Topics

bioinformatics evolution evolutionary-biology genomics phylogenetics phylogenomics python systematics

Created almost 6 years ago · Last pushed 7 months ago

Metadata Files

Readme License

Run ClipKIT in the browser and leave the computing up to us!

ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others.

If you found clipkit useful, please cite ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference. Steenwyk et al. 2020, PLOS Biology. doi: 10.1371/journal.pbio.3001007.

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

Quick Start

```shell

install

pip install clipkit

run

clipkit input.fa ```

Installation

If you are having trouble installing ClipKIT, 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: ```shell

create virtual environment

python -m venv venv

activate virtual environment

source venv/bin/activate

install clipkit

pip install clipkit ``` Note, the virtual environment must be activated to use clipkit.

After using ClipKIT, 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/ClipKIT.git cd ClipKIT/

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 clipkit.

To install via anaconda, execute the following command:

shell conda install bioconda::clipkit Visit here for more information: https://anaconda.org/bioconda/clipkit

Owner

Name: Jacob L. Steenwyk
Login: JLSteenwyk
Kind: user
Location: Berkeley, CA
Company: University of California, Berkeley

Website: https://jlsteenwyk.com
Twitter: JLSteenwyk
Repositories: 10
Profile: https://github.com/JLSteenwyk

Berkeley Science Fellow and Postdoctoral Scholar. Evolutionary genomics and software development.

GitHub Events

Total

Create event: 5
Release event: 2
Issues event: 8
Watch event: 16
Issue comment event: 13
Push event: 27
Pull request event: 2
Fork event: 1

Last Year

Create event: 5
Release event: 2
Issues event: 8
Watch event: 16
Issue comment event: 13
Push event: 27
Pull request event: 2
Fork event: 1

Committers

Last synced: 8 months ago

All Time

Total Commits: 270
Total Committers: 7
Avg Commits per committer: 38.571
Development Distribution Score (DDS): 0.452

Past Year

Commits: 4
Committers: 1
Avg Commits per committer: 4.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
JLSteenwyk	j**k@g**m	148
Thomas Buida	t**a@g**m	46
Jacob Steenwyk	j**k@J**y	37
Jacob Steenwyk	j**k@J**t	21
dependabot[bot]	4****]	8
Jacob Steenwyk	j**k@J**l	8
Jacob L Steenwyk	j**k@J**l	2

Committer Domains (Top 20 + Academic)

jacobs-mbp.attlocal.net: 1 jacobs-mbp.pavlov.gateway: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 22
Total pull requests: 45
Average time to close issues: 6 days
Average time to close pull requests: 23 days
Total issue authors: 18
Total pull request authors: 3
Average comments per issue: 2.77
Average comments per pull request: 0.27
Merged pull requests: 25
Bot issues: 0
Bot pull requests: 26

Past Year

Issues: 5
Pull requests: 6
Average time to close issues: 20 days
Average time to close pull requests: 5 minutes
Issue authors: 4
Pull request authors: 1
Average comments per issue: 2.4
Average comments per pull request: 0.0
Merged pull requests: 4
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

edgardomortiz (2)
vagkaratzas (2)
chtsai0105 (2)
sanyalab (2)
sen-pai (1)
nbat64 (1)
jsharbrough (1)
ialbert (1)
atongsa (1)
jolienvanhooff (1)
smorzechowski (1)
naturepoker (1)
haruosuz (1)
zhangwenda0518 (1)
LifeMine-swyka (1)

Pull Request Authors

dependabot[bot] (35)
JLSteenwyk (17)
TJBIII (5)

Top Labels

Issue Labels

bug (7) question (3) enhancement (3)

Pull Request Labels

dependencies (35) codex (1)

Packages

Total packages: 1
Total downloads:
- pypi 497 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 47
Total maintainers: 1

pypi.org: clipkit

Alignment trimming software for phylogenetics.

Homepage: https://github.com/jlsteenwyk/clipkit
Documentation: https://clipkit.readthedocs.io/
License: mit
Latest release: 2.5.1
published 7 months ago

Versions: 47
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 497 Last month
Docker Downloads: 0

Rankings

Docker downloads count: 2.3%

Stargazers count: 9.9%

Dependent packages count: 10.1%

Average: 12.9%

Downloads: 16.8%

Forks count: 16.9%

Dependent repos count: 21.6%

Maintainers (1)

JLSteenwyk

Last synced: 7 months ago

Dependencies

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docs/requirements_manual.txt pypi

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requirements.txt pypi

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six ==1.14.0
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wcwidth ==0.1.9
zipp ==3.1.0

.github/workflows/ci.yml actions

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cython ==0.29.16
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wcwidth ==0.1.9
webencodings ==0.5.1
wrapt ==1.11.2

clipkit

Science Score: 49.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Run ClipKIT in the browser and leave the computing up to us!

install

run

create virtual environment

activate virtual environment

install clipkit

deactivate virtual environment

download

create virtual environment

activate virtual environment

install

deactivate virtual environment

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: clipkit

Rankings

Maintainers (1)

Dependencies