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MLTreeMap - Accurate Maximum Likelihood Placement Of Environmental DNA Sequences Into Taxonomic And Functional Reference Phylogenies

Manuel Stark, Simon A Berger, Alexandros Stamatakis, Christian von Mering

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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.