The metagenomics RAST server is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the (Rapid Annotation using Subsystem Technology (RAST) server. The RAST technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data and has been adapted for metagenome analysis. The server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes.