Pairwise DNA sequence alignment is achieved by adding gaps (-) into sequences, so two sequences are aligned each other according to their homology. Two bases aligned in the same column are thought to have a common ancestor. Pairwise sequence alignment can be carried out using a variety of computer programs based on different algorithms and run parameters. It is, therefore, possible that different software tools may produce different alignments.
16S rRNA gene sequence similarity has been widely used in classification and identification of Bacteria and Archaea. For taxonomic purposes, we have used the global alignment algorithm of Myers and Miller (1988). This method has been used in the EzBioCloud (formerly EzTaxon) service and the calculation of proposed similarity cutoff, i.e., 98.7%, for bacterial species boundary (Kim et al., 2014). The online alignment tool for Myers and Miller’s algorithm is provided at http://www.ezbiocloud.net/tools/pairAlign.