MG-RAST is an open-source web application server that suggests automatic phylogenetic and functional analysis of metagenomes. It is also one of the biggest repositories for metagenomic data. The name is an abbreviation of Metagenomic Rapid Annotations using Subsystems Technology.The pipeline automatically produces functional assignments to the sequences that belong to the metagenome by performing sequence comparisons to databases in bothnucleotide and amino-acid levels. The applications supplies phylogenetic and functional assignments of the metagenome being analysed, as well as tools for comparing different metagenomes. It also provides a RESTful API for programmatic access.