The Jukes and Cantor 1969 (JC69) distance is calculated as \(-\frac{3}{4} \ln(1 - \frac{4}{3} p )\), where \(p\) is the sum of the probabilities of the alignment. See the Wikipedia for more details.
Arguments
- train_parameters
A list containing the probabilities of the alignment, produced by the
readTrainFile()function.
Value
Returns a numeric value show the evolutionary distance between two genomes. the larger the value, the more different the two genomes are.
References
Jukes, T.H. & Cantor, C.R. (1969). "Evolution of protein molecules." In Mammalian Protein Metabolism (pp. 21–132). Academic Press.
See also
Other Similarity indexes:
GOC(),
K80_distance(),
T92_distance(),
correlation_index(),
karyotype_index(),
slidingWindow(),
strand_randomisation_index(),
synteny_index()
Examples
parameters <- readTrainFile(system.file("extdata/example.train", package = "GenomicBreaks"))
JC69_distance(parameters)
#> [1] 0.0161481