0.04
0.02
0.06
0.9
0.96
0.062886
0.04
0.02
0.06
0.9
0.96
0.062886
The Kimura 2-Parameter (K2P) Distance calculator estimates evolutionary distance between nucleotide sequences by distinguishing between transitions and transversions. Unlike the simpler Jukes-Cantor model that treats all substitutions equally, the K2P model recognizes that transitions (purine-to-purine or pyrimidine-to-pyrimidine changes) occur more frequently than transversions (purine-to-pyrimidine or vice versa).
This model is one of the most widely used distance measures in molecular phylogenetics, particularly for DNA barcoding and constructing neighbor-joining trees. It provides a more accurate estimate of evolutionary distance for most real-world nucleotide data.
The calculator first determines the proportions of transitions (P) and transversions (Q):
P = Transitions / Total Sites
Q = Transversions / Total Sites
The Kimura 2-Parameter distance is then computed as:
d = -1/2 × ln(1 - 2P - Q) - 1/4 × ln(1 - 2Q)
This formula separately corrects for multiple transitions and transversions, yielding a more accurate distance estimate when the transition/transversion ratio differs from 0.5.
Inputs
Results
With 20 transitions and 10 transversions out of 500 sites, the K2P distance is 0.0626, reflecting a 2:1 transition-to-transversion ratio typical of many organisms.
Inputs
Results
With a strong transition bias (4:1 ratio), the corrected distance is 0.229, demonstrating how the K2P model accounts for the different rates of substitution types.
Use K2P when your sequences show a transition/transversion bias, which is the case for most real nucleotide data. The Jukes-Cantor model is only appropriate when all substitution types occur at equal rates. Since transitions almost always outnumber transversions in nature, K2P is generally the better default choice.
The transition/transversion ratio (Ti/Tv) compares the frequency of transitions (A to G, C to T) to transversions (A to C, A to T, G to C, G to T). In most organisms this ratio ranges from 2:1 to over 10:1 for mitochondrial DNA, reflecting the biochemical ease of transitions compared to transversions.
The K2P model still assumes equal base frequencies and uniform rates across sites. For sequences with strong compositional biases or rate variation among sites, more complex models like Tamura-Nei or General Time Reversible (GTR) may be more appropriate. The model also becomes unreliable at very high divergence levels.
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