0.05
95
%
0.05
95
%
The Pairwise Distance Calculator computes the simplest measure of genetic distance between two sequences: the proportion of sites that differ. Also known as the p-distance or Hamming distance normalized by sequence length, this metric provides an uncorrected estimate of evolutionary divergence between aligned sequences.
While more sophisticated models exist, the p-distance remains valuable for its simplicity and as a starting point for evolutionary analyses. It is particularly useful for closely related sequences where the probability of multiple substitutions at a single site is low, and it serves as input for many correction formulas.
The pairwise distance is the ratio of mismatched positions to total sites compared:
Distance = Mismatches / Total Sites
The complementary sequence identity is:
Identity (%) = (1 - Distance) × 100
This is the most basic evolutionary distance metric and does not correct for multiple substitutions at the same site. For closely related sequences, the p-distance is a good approximation of the true distance.
Inputs
Results
With 25 mismatches out of 500 sites, the p-distance is 0.05, corresponding to 95% sequence identity, typical for closely related strains of the same species.
Inputs
Results
At 20% divergence, the sequences are moderately different. At this level, corrected distance measures like Jukes-Cantor would start to deviate noticeably from the p-distance.
The p-distance is preferred for very closely related sequences where multiple substitutions at the same site are unlikely. It is also used as a quick initial assessment and when model assumptions of correction methods cannot be verified. Some phylogenetic methods like neighbor-joining can work well with p-distances for closely related taxa.
Because some sites may have mutated multiple times during evolution. A site that changed from A to G and then back to A appears identical in the comparison but actually experienced two substitutions. This back-mutation effect becomes more pronounced at higher divergence levels.
This depends on your analysis. In many cases, gap positions are excluded entirely from the comparison (complete deletion or pairwise deletion). Some analyses treat gaps as a fifth character state and count them as mismatches. The chosen approach should be clearly stated in your methods.
Roboculator Team
The Roboculator Team explains calculations, planning tools, and practical formulas in clear language for real-life situations.
How helpful was this calculator?
Be the first to rate!
