PhymmBL (rhymes with “thimble”), the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy. Phymm, a new classification approach for metagenomics data which uses interpolated Markov models (IMMs) to taxonomically classify DNA sequences, can accurately classify reads as short as 100 bp. Its accuracy for short reads represents a significant leap forward over previous composition-based classification methods.
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A. Brady and S. L. Salzberg.
Phymm and PhymmBL: Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models.
Nature Methods Vol. 6, No. 9, pp. 673-676 (September 2009)