Jukes & Cantor

Jukes & Cantor (JC) is a method named after the scientists Jukes and Cantor for correcting distance data from a sequence alignment .

The raw distances can be used to construct a family tree . Then, however, it would be neglected that there are also reverse mutations (e.g. A → C → A). With larger evolutionary distances this would lead to drastic errors, because the distances would be regarded as too small. Jukes and Cantor therefore proposed a simple correction system in 1969, in which it is assumed that the probability of being exchanged during evolution is the same for every base. It is also assumed that all bases in the sequence occur approximately equally.

The actual number of mutations is calculated according to JC using the formula:

${\displaystyle \operatorname {JC} (a_{i},a_{j})=-{\frac {3}{4}}\cdot \ln \left[1-{\frac {4}{3}}\cdot \operatorname {Ham} \left(a_{i},a_{j}\right)\right]}$

where Ham is the uncorrected Hamming distance divided by the length of the sequence . That is, ham is the observed mutation rate of the sequences.

Jukes & Cantor simplifies a lot, which is no longer acceptable for most tasks. However, JC can still be used for closely related sequences if it can be assumed that there was only one mutation per base.

literature

• TH Jukes and C. Cantor, Mammalian Protein Metabolism , chapter Evolution of protein molecules , pages 21-132

Academic Press, New York, 1969.