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Analyze statistical significance of sample groupings (version
Only symmetric, hollow distance matrices may be used as input. Asymmetric distance matrices, such as those obtained by the UniFrac Gain metric (i.e. -m unifrac_g), should not be used as input
All methods except for BIO-ENV accept just a single category. If multiple categories are provided, only the first will be used
Only applies to adonis, ANOSIM, MRPP, PERMANOVA, PERMDISP, and db-RDA. Must be greater than or equal to zero

What it does

This script allows for the analysis of the strength and statistical significance of sample groupings using a distance matrix as the primary input. Several statistical methods are available: adonis, ANOSIM, BIO-ENV, Moran's I, MRPP, PERMANOVA, PERMDISP, and db-RDA.

Note: R's vegan and ape packages are used to compute many of these methods, and for the ones that are not, their implementations are based on the implementations found in those packages. It is recommended to read through the detailed descriptions provided by the authors (they are not reproduced here) and to refer to the primary literature for complete details, including the methods' assumptions. To view the documentation of a method in R, prepend a question mark before the method name. For example:

The following are brief descriptions of the available methods:

For more information and examples pertaining to this script, please refer to the accompanying tutorial, which can be found at

At least one file will be created in the output directory specified by -o. For most methods, a single output file containing the results of the test (e.g. the effect size statistic and p-value) will be created. The format of the output files will vary between methods as some are generated by native QIIME code, while others are generated by R's vegan or ape packages. Please refer to the script description for details on how to access additional information for these methods, including what information is included in the output files.

db-RDA is the only exception in that two output files are created: a results text file and a PDF of the ordination plot.