Not yet reviewed by Pith; the record is open.

Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows us to identify the sequenced community members and to reconstruct taxonomic bins with sequence data for the individual taxa. We describe an algorithm and the accompanying software, taxator-tk, which performs taxonomic sequence assignments by fast approximate determination of evolutionary neighbors from sequence similarities. Taxator-tk was precise in its taxonomic assignment across all ranks and taxa for a range of evolutionary distances and for short sequences. In addition to the taxonomic binning of metagenomes, it is well suited for profiling microbial communities from metagenome samples becauseit identifies bacterial, archaeal and eukaryotic community members without being affected by varying primer binding strengths, as in marker gene amplification, or copy number variations of marker genes across different taxa. Taxator-tk has an efficient, parallelized implementation that allows the assignment of 6 Gb of sequence data per day on a standard multiprocessor system with ten CPU cores and microbial RefSeq as the genomic reference data.