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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
+
+^^^^
+