Site-specific variability calculations are performed by HmtDB, using the SiteVar algorithm for nucleotide variability and the MitVarProt algorithm for aminoacid variability; in both cases calculations are based on healthy and pathologic genome datasets, as well as on the related continent-specific subsets.

The resulting variability score (nt_var) ranges from 0 to 1, with a higher value indicating a lower functional constraint of the site.