mothur – mothur is a bioinformatics tool for analyzing 16S rRNA gene sequences.
MEGAN5 – MEGAN5 (MEta Genome ANalyzer) is an analysis tool for metagenomic of short-read data.
ESPRIT – ESPRIT (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.
QIIME – QIIME (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.