Overview

If you have purchased the PERMANOVA+ add-on, then you will have an additional menu item that allows you to perform a broad range of additional analyses using a suite of routines that are not available in the base PRIMER 7 package, including PERMANOVA, PERMDISP, PCO, DISTLM/dbRDA and CAP. See the PERMANOVA+ user manual for details regarding these routines and the underlying methods.
Here, we will run through a quick example of how to set up and run a multi-factor PERMANOVA analysis in PRIMER. Permutational multivariate analysis of variance (PERMANOVA) partitions variation in the space of a chosen dissimilarity measure in response to one or more factors in a specified sampling protocol or experimental design (
 Anderson (2001a)
 , 
 Anderson (2017)
 ). Tests of individual terms in a PERMANOVA model are achieved by constructing correct (pseudo-)F ratios on the basis of expectations of mean squares (EMS), and p-values are obtained using correct permutation algorithms given the full study design.
Importantly, the PERMANOVA routine in PRIMER allows the user:

to specify whether factors are fixed or random,
to specify whether a factor is nested in one or more other factors,
to test interaction terms,
to include one or more quantitative covariates in the analysis,
to remove individual terms from a model or to perform pooling,
to handle correctly:

mixed models

user-specified contrasts

BACI designs (before-after/control-impact),

asymmetrical designs (e.g., in environmental impact studies),

randomised blocks,

split plots,

hierarchical designs,

repeated measures,

unbalanced designs (Type I, II or III sums of squares),
... and more.