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All QIIME analyses are performed using python (.py) scripts. See the QIIME install guide if you need help getting the QIIME scripts installed.
All QIIME scripts can take the -h option to provide usage information. You can get this information for the align_seqs.py script (for example) by running:
The same documentation that is presented when calling a script with -h is available for all QIIME scripts at the links below.
Scripts in the biom-format project provide functionality for working with biom tables generated in QIIME.
Other documentation of the biom-format project can be found at www.biom-format.org.
biom-format is a dependency of QIIME, so these scripts should already be available in your QIIME environment.
Scripts in the emperor project provide functionality for generating interactive 3D ordination plots from QIIME ordination results.
Other documentation of the emperor project can be found at biocore.github.io/emperor.
emperor is a dependency of QIIME, so these scripts should already be available in your QIIME environment.