is implemented in MEGAN. Another tool, PhymmBL, uses interpolated Markov models to assign reads. MetaPhlAn and AMPHORA are methods based on unique clade-specific markers for estimating organismal relative abundances with improved computational performances. Other tools, like mOTUs and MetaPhyler, use universal marker genes to profile prokaryotic species. With the mOTUs profiler is possible to profile species without a reference genome, improving the estimation of microbial community diversity. Recent methods, such as SLIMM, use read coverage landscape of individual reference genomes to minimize false-positive hits and get reliable relative abundances. In composition based binning, methods use intrinsic features of the sequence, such as oligonucleotide frequencies or codon usage bias. Once sequences are binned, it is possible to carry out comparative analysis of diversity and richness. Data integration The massive amount of exponentially growing sequence data is a daunting challenge that is complicated by the complexity of the metadata associated with metagenomic projects. Metadata includes detailed information about the three-dimensional (including depth, or height) geography and environmental features of the sample, physical data about the sample site, and the methodology of the sampling. This information is necessary both to ensure replicability and to enable downstream analysis. Because of its importance, metadata and collaborative data review and curation require standardized data formats located in specialized databases, such as the Genomes OnLine Database (GOLD). Several tools have been developed to integrate metadata and sequence data, allowing downstream comparative analyses of different datasets using a number of ecological indices. In 2007, Folker Meyer and Robert Edwards and a team at Argonne National Laboratory and the University of Chicago released the Metagenomics Rapid Annotation using Subsystem Technology server (MG-RAST) a community resource for metagenome data set analysis. As of June 2012 over 14.8 terabases (14x1012 bases) of DNA have been analyzed, with more than 10,000 public data sets freely available for comparison within MG-RAST. Over 8,000 users now have submitted a total of 50,000 metagenomes to MG-RAST. The Integrated Microbial Genomes/Metagenomes (IMG/M) system also provides a collection of tools for functional analysis of microbial communities based on their metagenome sequence, based upon reference isolate genomes included from the Integrated Microbial Genomes (IMG) system and the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. One of the first standalone tools for analysing high-throughput metagenome shotgun data was MEGAN (MEta Genome ANalyzer). A first version of the program was used in 2005 to analyse the metagenomic context of