MetaPhyler is a novel taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. Our classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. Our reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database. Results on simulated metagenomic datasets demonstrate that MetaPhyler outperforms previous tools used in this context (CARMA, MEGAN and PhymmBL).
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BMC Genomics. 2011;12 Suppl 2:S4. Epub 2011 Jul 27.
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.
Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M.