Calypso is an easy to use online software, allowing non expert users to mine, interpret and compare taxonomic information from metagenomic datasets, with a focus on microbiome-environment associations. Powerful visualization techniques are provided, generating high quality figures that can readily be used in scientific publications. Robust and thorough analyses of large taxonomic datasets can be rapidly obtained, without scripting or programming skills, via a broad range of algorithms for clustering, classification and statistical testing.