Comparison of different taxonomic classification methods. (a) Average performance per contig for the simMC data set (average length 2332 bp) at genus rank in four different experiments. Each experiment reflects a different scenario in terms of available reference sequences from closely related organisms for the dominant strains. ‘Known species’ had complete genome sequences of the same species available as reference; in the other experiments sequences of the same clades at the respective rank were excluded, while retaining 100 kb of the dominant strains. (b) Scaffold-contig consistency for the WG-1 population (uncultured Succinivibrionaceae bacterium) of the Tammar wallaby gut metagenome. Contig coloring reflects taxonomic assignment consistency with respect to WG-1. Only scaffolds longer than 20 kb are shown. (c) Empirical execution time evaluated on a Linux machine with 3 GHz processor and 4 GB main memory. Results for MEGAN and PhymmBL were determined with a reference database of size 2.1 GB.