METAREP provides a suite of web based tools to help scientists to view, query, browse and compare metagenomic annotation data derived from ORFs called on metagenomics reads or assemblies. METAREP supports browsing of functional and taxonomic assignments. Users can either specify fields, or logical combinations of fields to filter and refine datasets. Users can compare multiple datasets at various functional and taxonomic levels applying statistical tests as well as hierarchical clustering, multidimensional scaling and heatmaps. For each of these features users can export tab delimited files for downstream analysis. The web site is optimized to be user friendly and fast