MetaCV is a composition and phylogeny-based algorithm to classify very short metagenomic reads (75-100 bp) into specific taxonomic and functional groups. It performs (for both sensitivity and specificity) as good as BlastX-based methods on simulated short reads, but runs 300 times faster, thus provides fast and accurate analysis on huge amount of NGS data.
If you publish research that uses metacv you have to cite it as follows: Liu JM, Wang HF, Yang HX, Zhang YZ, Wang JF, Zhao FQ, Qi J. Composition based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms. Nucleic Acids Research 2012.