QIIME  (an abbreviation for Quantitative Insights Into Microbial Ecology) is a bioinformatic pipeline designated for the task of analysing microbial communities that were sampled through marker gene (e.g. 16S or 18S rRNA genes) amplicon sequencing. In its heart the pipeline performs quality control over the input sequencing reads, clusters the marker gene nucleotide sequences at a requested phylogenetic level (e.g. 97% for species level) into OTUs (operational taxonomic units) and taxonomically annotates the OTUs by looking for sequences similar to them on a reference taxonomic database. The main output from the QIIME pipeline is the OTU table, which describes the microbial OTUs and their abundances in each of the samples. Additional tools that are relevant to ecological aspects of the samples being investigated are also provided within the pipeline, including rarefaction, beta diversity assessment, principle coordinates analysis (PCoA) and much more. QIIME presents a very modular approach and allows multiple methods to be applied in many stages of the analysis. For example, the stage of sequences clustering can be performed using either UCLUST, CD-HIT, BLAST and more. QIIME is under active development since its release in 2010.