title: Methods for comparative metagenomics.
abstract: BACKGROUND
  Metagenomics is a rapidly growing field of research that aims at studying uncultured organisms to understand the true diversity of microbes, their functions, cooperation and evolution, in environments such as soil, water, ancient remains of animals, or the digestive system of animals and humans. The recent development of ultra-high throughput sequencing technologies, which do not require cloning or PCR amplification, and can produce huge numbers of DNA reads at an affordable cost, has boosted the number and scope of metagenomic sequencing projects. Increasingly, there is a need for new ways of comparing multiple metagenomics datasets, and for fast and user-friendly implementations of such approaches.
  
  
  RESULTS
  This paper introduces a number of new methods for interactively exploring, analyzing and comparing multiple metagenomic datasets, which will be made freely available in a new, comparative version 2.0 of the stand-alone metagenome analysis tool MEGAN.
  
  
  CONCLUSIONS
  There is a great need for powerful and user-friendly tools for comparative analysis of metagenomic data and MEGAN 2.0 will help to fill this gap.
authors.affiliation: Center for Bioinformatics ZBIT, Tübingen University, Sand 14, 72076 Tübingen, Germany. huson@informatik.uni-tuebingen.de
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Huson
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Richter
authors.forename: Suparna
authors.initials: S
authors.lastname: Mitra
authors.forename: Alexander F
authors.initials: AF
authors.lastname: Auch
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
mesh_terms: D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D012984:Software