# 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](https://learninghub.primer-e.com/link/227), [PERMDISP](https://learninghub.primer-e.com/link/269), [PCO](https://learninghub.primer-e.com/link/282), [DISTLM/dbRDA](https://learninghub.primer-e.com/link/291) and [CAP](https://learninghub.primer-e.com/link/307). See the [PERMANOVA+ user manual](https://learninghub.primer-e.com/books/permanova-for-primer-guide-to-software-and-statistical-methods) 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 ({{@483#bkmrk-anderson2001a}}, {{@483#bkmrk-anderson2017}}). 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.