mothurmothur is a bioinformatics tool for analyzing 16S rRNA gene sequences.

MEGAN5MEGAN5 (MEta Genome ANalyzer) is an analysis tool for metagenomic of short-read data.

ESPRITESPRIT (Estimating Species Richness Using Large Collections of 16S rRNA Pyrosequences) is a new algorithm for classifying large collections of 16S ribosomal sequences which addresses several computational limitations of prior methods.

QIIMEQIIME (Quantitative Insights Into Microbial Ecology) is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data.

USEARCH – High-throughput search and clustering.

Silva – The Silva database is a comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data.