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.. _scripts: Script Index
==================================
Scripts - Analyses and Parameters
==================================
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>`_.
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