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Mothur (https://mothur.org) is one such in‐silico tool that is now being widely used for the analysis of sequence generated by Sanger and/or 454 ribosomal pyro‐tag sequencing (Patrick et al. 2009). Dr. Patrick Schloss and his research group in the Department of Microbiology and Immunology at University of Michigan initiated Mothur in order to develop a single piece of open‐source, expandable software that could be able to fill the bioinformatics needs of the microbial ecology community. Since its development, this tool has helped several metagenome researchers and has become among the most cited in‐silico tools to generate a meaningful information from 16s rRNA sequences.

Similarly, other bioinformatics tools, such as QIIME and MEGEN are also being widely utilized by research community to analyze metagenomic data.