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Open Access Highly Accessed Methodology article

MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

Manuel Stark12, Simon A Berger3, Alexandros Stamatakis3 and Christian von Mering1*

Author Affiliations

1 Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland

2 Ph.D. program in Molecular Life Sciences, University of Zurich and Federal Institute of Technology (ETH), Zurich, Switzerland

3 The Exelixis Lab, Department of Computer Science, Technische Universität München, Germany

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BMC Genomics 2010, 11:461  doi:10.1186/1471-2164-11-461

Published: 5 August 2010



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.


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'; webcite) uses raw nucleotide sequences as input, and includes hand-curated, extensible reference information.


We discuss how we validated our pipeline using complete genomes as well as simulated and actual environmental sequences.