When reference sequences are provided, this service will calculate exact pairwise similarities between query and reference sequences under the recommended settings proposed by Meier-Kolthoff et al. (2013). To the best of our knowledge these are currently the only settings which allow for the application of phylum-specific 16S similarity thresholds as introduced earlier by Meier-Kolthoff et al. (2013). Additionally, a maximum-likelihood as well as maximum-parsimony phylogeny from all uploaded sequences is inferred, including bootstrapping. When no reference sequences are uploaded, pairwise similarities are skipped. The results are sent by e-mail, including publication-ready description text. Instead of gene sequences, protein sequences can also be uploaded, but only as FASTA files, and without calculation of pairwise similarities. For further details see the gene phylogeny FAQ page.