title: MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies.
abstract: BACKGROUND
  Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem.
  
  
  RESULTS
  Existing algorithms are largely optimized for speed and coverage; in contrast, we present here a software framework that focuses on a restricted set of informative gene families, using Maximum Likelihood to assign these with the best possible accuracy. This framework ('MLTreeMap'; http://mltreemap.org/) uses raw nucleotide sequences as input, and includes hand-curated, extensible reference information.
  
  
  CONCLUSIONS
  We discuss how we validated our pipeline using complete genomes as well as simulated and actual environmental sequences.
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland.
authors.forename: Manuel
authors.initials: M
authors.lastname: Stark
authors.forename: Simon A
authors.initials: SA
authors.lastname: Berger
authors.forename: Alexandros
authors.initials: A
authors.lastname: Stamatakis
authors.forename: Christian
authors.initials: C
authors.lastname: von Mering
mesh_terms: D000465:Algorithms; D004247:DNA / Q000032:analysis* / Q000145:classification / Q000235:genetics; D020407:Internet; D016013:Likelihood Functions; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D012985:Software Design
chemical_list: D004247:DNA