clipkit 2.14.0

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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.

This documentation covers downloading and installing ClipKIT. Details about each function as well as tutorials for using ClipKIT are available in the online documentation. Release automation details are documented in RELEASE.md.

Quick Start

# install
pip install clipkit
# run
clipkit input.fa

# mask all in-frame stops in a codon-aligned nucleotide MSA
clipkit coding.fa --codon --sequence_type nt --remove_stop_codons all

# fractionally weight IUPAC ambiguity symbols in entropy/composition analyses
clipkit ambiguous.fa --sequence_type nt --ambiguity_handling fractional

ClipKIT handles recognized IUPAC ambiguity symbols conservatively by default: they are treated as missing evidence and contribute to the effective unavailable fraction used by gap-based modes. Use fractional to distribute them across possible states for entropy, composition, and the clade-entropy part of heterotachy analysis, or literal for legacy behavior. Configured gap characters take precedence, and alignment symbols are never rewritten. See the ambiguity-handling documentation for the full nucleotide/protein mappings and mode-specific behavior.

The same operation is available through the Python API:

from clipkit import clipkit

trim_run, stats = clipkit(
    input_file_path="coding.fa",
    mode="gappy",
    gaps=0.9,
    sequence_type="nt",
    codon=True,
    remove_stop_codons="all",
)
print(trim_run.stop_codon_masking.summary)

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 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.

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:

# 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:

# 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/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:

# deactivate virtual environment
deactivate

Note: the virtual environment must be activated to use clipkit.

To install via anaconda, execute the following command:

conda install bioconda::clipkit

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