.. _scripts: Script Index

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Scripts - Analyses and Parameters
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All QIIME analyses are performed using python (.py) scripts, which are located in the your QIIME scripts directory. To access QIIME python scripts, this directory should be in your ``$PATH`` environment variable. You should have `set this up during installation <../install/install.html#set-script-dir>`_ (unless you're using the virtual box, in which case it was already set up).

You can then call QIIME scripts as::

	python align_seqs.py -h

All QIIME scripts can take the ``-h`` option to provide usage information.

An `index of the QIIME scripts is provided here <../scripts/index.html>`_.
