clipkit 2.10.2
Alignment trimming software for phylogenetics.
Requires Python: >=3.10

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<center><h2>Run <a href="https://clipkit.genomelybio.com/">ClipKIT in the browser</a> and leave the computing up to <a href="https://www.genomelybio.com/">us</a>!</h2></center>
<br />

ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others.<br /><br />
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).

<br /><br />

---

<br />

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/).

<br />

**Quick Start**

```shell
# install
pip install clipkit
# run
clipkit input.fa
```

**eComp archives**

ClipKIT can trim Evolutionary Compression (`.ecomp`) archives directly. Simply
pass the `.ecomp` file to the CLI, and ClipKIT will unpack its metadata sidecar
and native payload before trimming the alignment. Archives encoded with zstd
require the optional [`zstandard`](https://pypi.org/project/zstandard/) module;
all other payload encodings work out of the box. By default the trimmed
alignment is written back as an `.ecomp` archive (with a gzip fallback payload);
specify `-of fasta` if you prefer a text format.

<br />

**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
```

<br />

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*.**

<br />

To install via anaconda, execute the following command:

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