SIMPER (Similarity Percentage) is a simple method for assessing which taxa are primarily responsible for an observed difference between groups of samples (Clarke 1993). The overall significance of the difference is often assessed by ANOSIM. The Bray-Curtis similarity measure (multiplied with 100) is most commonly used with SIMPER, but the Euclidean, cosine and chord measures can also be used.
If more than two groups are selected, you can either compare two groups (pairwise) by choosing from the lists of groups, or you can pool all samples to perform one overall multi-group SIMPER. In the latter case, all possible pairs of samples are compared using the Bray-Curtis measure. The overall average dissimilarity is computed using all the taxa, while the taxon-specific dissimilarities are computed for each taxon individually.
Samples go in rows, grouped with a group column, and taxa in columns. In the output table, taxa are sorted in descending order of contribution to group difference. The last three columns show the mean abundance in each of the groups.
Missing data supported by column average substitution.
Reference
Clarke, K.R. 1993. Non-parametric multivariate analysis of changes in community structure. Australian Journal of Ecology 18:117-143.