Evaluation of classification performance Comparison of phylogenetic classification performance of MetaPhyler, MEGAN, CARMA and PhymmBL. The sensitivity and precision are calculated across five taxonomic levels using 60bp and 300bp simulated metagenomic reads. During the classification with MetaPhyler, MEGAN, and PhymmBL, reference sequences that are from the same genome as the query reads are excluded. CARMA results are from the classifications based on WebCARMA server. This figure shows that the sensitivity of MetaPhyler significantly outperforms the other three methods, and that the precision is also slightly better at the genus level.