Mercurial > repos > padge > clipkit
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author | padge |
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date | Fri, 25 Mar 2022 13:04:31 +0000 |
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.. image:: _static/img/ClipKIT_logo_top_only_v1.jpg :width: 55% :align: center :target: https://jlsteenwyk.com/ClipKIT ^^^^^ ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes those that display characteristics poor phylogenetic signal. 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: |doiLink|_. .. _doiLink: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001007 .. |doiLink| replace:: 10.1371/journal.pbio.3001007 Quick Start ----------- **1) Installation** To help ensure ClipKIT can be installed using your favorite workflow, we have made ClipKIT available from pip, source, and the anaconda cloud. **Install from pip** To install from pip, use the following commands: .. code-block:: 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.** | **Install from source** Similarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands: .. code-block:: shell # download git clone https://github.com/JLSteenwyk/ClipKIT.git cd PhyKIT/ # 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: .. code-block:: shell # deactivate virtual environment deactivate **Note, the virtual environment must be activated to use clipkit.** .. code-block:: shell git clone https://github.com/JLSteenwyk/ClipKIT.git cd ClipKIT/ make install If you run into permission errors when executing *make install*, create a virtual environemnt for your installation: .. code-block:: shell git clone https://github.com/JLSteenwyk/ClipKIT.git cd ClipKIT/ python -m venv .venv source .venv/bin/activate make install Note, the virtual environment must be activated to use clipkit. | **Install from anaconda** To install via anaconda, execute the following command: .. code-block:: shell conda install -c jlsteenwyk clipkit Visit here for more information: https://anaconda.org/jlsteenwyk/clipkit | **2) Usage** To use ClipKIT in its simpliest form, execute the following command: .. code-block:: shell clipkit <input> Output file with the suffix ".clipkit" | ^^^^ .. toctree:: :maxdepth: 4 about/index advanced/index performance_assessment/index change_log/index other_software/index frequently_asked_questions/index ^^^^