PERMANOVA Analysis
PERMANOVA Analysis (PERmutational Multivariate ANalysis Of VAriance, also known as non-parameteric MANOVA [Anderson, 2001]), can be used to measure effect size and significance on beta diversity for a grouping variable. For example, it can be used to show whether OTU abundance profiles of replicate samples taken from different locations vary significantly according to the location or not. The significance is obtained by a permutation test.
To perform a PERMANOVA analysis, go to:
Toolbox | Microbial Genomics Module (
) | OTU clustering (
) | PERMANOVA Analysis (
)
Choose an OTU abundance table as input. In the next wizard window you can specify the phylogenetic tree reconstructed from the alignment of the most abundant OTUs in the previous step and select the beta-diversity and the phylogenetic diversity measures you wish to use for this analysis (see Beta diversity measures).
The output of the analysis is a report which contains 2 tables for each beta diversity measure used:
- A table showing the metadata variable used, its groups and the results of the test (pseudo-f-statistic and p-value)
- A PERMANOVA analysis for each pair of groups and the results of the test (pseudo-f-statistic and p-value). Bonferroni-corrected p-values (which correct for multiple testing) are also shown.