ANOSIM (ANalysis Of Similarities) is a non-parametric test of significant difference between two or more groups, based on any distance measure (Clarke 1993). The distances are converted to ranks. ANOSIM is normally used for taxa-in-samples data, where groups of samples are to be compared. Items go in rows, variates in columns, and groups should be specified with a group column as usual.
In a rough analogy with ANOVA, the test is based on comparing distances between groups with distances within groups. See the Past manual for mathematical details.
Large positive R (up to 1) signifies dissimilarity between groups. The one-tailed significance is computed by permutation of group membership, with 9,999 replicates (can be changed).
Pairwise ANOSIMs between all pairs of groups are provided as a post-hoc test. Significant comparisons (at p<0.05) are shown in pink. The optional Bonferroni correction multiplies the p values with the number of comparisons. This correction is very conservative (produces large p values). The sequential Bonferroni option does not output corrected p values, but significance is decided based on step-down sequential Bonferroni, which is slightly more powerful than simple Bonferroni.
Missing data supported by pairwise deletion (not for the Raup-Crick, Rho and user-defined indices).
Reference
Clarke, K.R. 1993. Non-parametric multivariate analysis of changes in community structure. Australian Journal of Ecology 18:117-143.