The Kimura's 2-parameter (K80) distance distinguishes between transitions and transversions. It is calculated as \(-\frac{1}{2} \ln\left(\left(1 - 2p - q\right) \times \sqrt{1 - 2q}\right)\), where \(p\) is the probability of transition and \(q\) is the probability of transversion. 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
Kimura, M. (1980). "A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences." Journal of Molecular Evolution, 16, 111–120. DOI: 10.1007/BF01731581
See also
Other Similarity indexes:
GOC(),
JC69_distance(),
T92_distance(),
correlation_index(),
karyotype_index(),
slidingWindow(),
strand_randomisation_index(),
synteny_index()
Examples
parameters <- readTrainFile(system.file("extdata/example.train", package = "GenomicBreaks"))
K80_distance(parameters)
#> [1] 0.01616738