LEfSe (Linear discriminant analysis Effect Size) determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance. LEfSe is available as a Galaxy module, and as a bitbucket repository. For additional information, please refer to the LEfSe paper. We provide support for LEfSe users. Please join our Google group designated specifically for LEfSe users. Feel free to post any questions on the google group by posting directly or emailing firstname.lastname@example.org.
See LEfSe wiki