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https://github.com/jlsteenwyk/clipkit
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
https://github.com/jlsteenwyk/clipkit
bioinformatics evolution evolutionary-biology genomics phylogenetics phylogenomics python systematics
Last synced: about 19 hours ago
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a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
- Host: GitHub
- URL: https://github.com/jlsteenwyk/clipkit
- Owner: JLSteenwyk
- License: mit
- Created: 2020-04-11T14:41:10.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2024-07-15T19:38:59.000Z (3 months ago)
- Last Synced: 2024-10-02T19:40:28.678Z (about 19 hours ago)
- Topics: bioinformatics, evolution, evolutionary-biology, genomics, phylogenetics, phylogenomics, python, systematics
- Language: Python
- Homepage: https://jlsteenwyk.com/ClipKIT/
- Size: 25.8 MB
- Stars: 61
- Watchers: 7
- Forks: 4
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- Changelog: change_log.txt
- License: LICENSE.md
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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](https://jlsteenwyk.com/publication_pdfs/2020_Steenwyk_etal_PLOS_Biology.pdf).
---
This documentation covers downloading and installing ClipKIT. Details about each function as well as tutorials for using ClipKIT are available in the [online documentation](https://jlsteenwyk.com/ClipKIT/).
**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](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 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