.. _cli:

Command-line interface
======================

.. contents::
	:depth: 2
	:local:
	:backlinks: none


ProPhyle – the main program
---------------------------

``prophyle``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	.. include:: reference/main.txt
		:code: text

``prophyle download``
^^^^^^^^^^^^^^^^^^^^^
	.. include:: reference/download.txt
		:code: text

``prophyle index``
^^^^^^^^^^^^^^^^^^
	.. include:: reference/index.txt
		:code: text

``prophyle classify``
^^^^^^^^^^^^^^^^^^^^^
	.. include:: reference/classify.txt
		:code: text

``prophyle compress``
^^^^^^^^^^^^^^^^^^^^^
	.. include:: reference/compress.txt
		:code: text

``prophyle decompress``
^^^^^^^^^^^^^^^^^^^^^^^
	.. include:: reference/decompress.txt
		:code: text

``prophyle_assembler``
----------------------
	.. include:: reference/prophyle_assembler.txt
		:code: text

``prophyle_index``
------------------

	.. include:: reference/prophyle_index.txt
		:code: text

	.. include:: reference/prophyle_index.txt_build.txt
		:code: text

	.. include:: reference/prophyle_index.txt_query.txt
		:code: text


``prophyle_assignment``
-----------------------

	.. include:: reference/prophyle_assignment.py.txt
		:code: text

``prophyle_propagation_makefile.py``
------------------------------------

	.. include:: reference/prophyle_propagation_makefile.py.txt
		:code: text

``prophyle_propagation_preprocessing.py``
-----------------------------------------

	.. include:: reference/prophyle_propagation_preprocessing.py.txt
		:code: text

``prophyle_propagation_postprocessing.py``
------------------------------------------

	.. include:: reference/prophyle_propagation_postprocessing.py.txt
		:code: text

``prophyle_validate_tree.py``
-----------------------------

	.. include:: reference/prophyle_validate_tree.py.txt
		:code: text