http://qiime.org/scripts/compare_categories.html
Description:

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:

?vegan::adonis

The following are brief descriptions of the available methods:

adonis - Partitions a distance matrix among sources of variation in order to describe the strength and significance that a categorical or continuous variable has in determining variation of distances. This is a nonparametric method and is nearly equivalent to db-RDA (see below) except when distance matrices constructed with semi-metric or non-metric dissimilarities are provided, which may result in negative eigenvalues. adonis is very similar to PERMANOVA, though it is more robust in that it can accept either categorical or continuous variables in the metadata mapping file, while PERMANOVA can only accept categorical variables. See vegan::adonis for more details.

We perform the adonis test because it is applicable to numeric and continuous variables.
