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, a Conda formula, a Docker image, and included in bioBakery (VM and cloud). For additional information, please refer to the LEfSe paper.

LEfSe can be installed with Conda or run from a Docker image. Please note, if you are using bioBakery (Vagrant VM or cloud) you do not need to install LEfSe because the tool and its dependencies are already installed.

Install with Conda: $ conda install -c bioconda lefse

Install with Docker: $ docker run -it biobakery/lefse bash

LEfSe requires R v. 3.6 or higher and the R libraries survival, mvtnorm, modeltools, coin, MASS.

We provide support for LEfSe users. Please join our bioBakery Support Forum designated specifically for LEfSe users.