Diversity analysis attempts to address questions like: how many species are
there in an ecosystem? how do these two ecosystems compare in terms of their
species?
The most common types of analysis are
alpha diversity and
beta diversity. Alpha diversity considers a
single sample to ask how many species it contains and how their abundances are
distributed. Beta diversity compares two samples.
The input data used for
diversity analysis is an OTU table. A tree is also
needed for Unifrac beta diversity analysis.
USEARCH supports diversity analysis through the
alpha_div command and beta_div command.