Table 1. The comparison of properties of taxonomical and functional analyses for metagenomic samples.

Features	Taxonomical analysis	Functional analysis
Input data types	Pyro-sequencing or shotgun sequencing data	shotgun sequencing data
Basic object sequences	16S rRNA sequences	Gene sequences
Reference databases	GreenGenes, RDP, Silva, etc.	NCBI NR, SEED. etc.
Basic results	Taxonomy structure (Qualitative and quantitative)	Functional hierarchy (Qualitative)
Extended results	Sample taxonomical structure comparison	Sample functional composition comparison, Functional and pathway enrichment
Applications	Novel strain identification	Gene discovery