The Tamura 1992 (T92) distance extends the K80 distance by taking GC content into account. It is calculated as \(-h \ln \left(1 - \frac{p}{h} - q\right) - \frac{1}{2} \times (1 - h) \ln\left(1 - 2 q\right)\), where \(p\) is the probability of transition, \(q\) the probability of transversion, \(h = 2\theta (1 - \theta)\) and \(\theta\) is the GC content. 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
Tamura, K. (1992). "Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases." Molecular Biology and Evolution, 9(4), 678–687. DOI: 10.1093/oxfordjournals.molbev.a040752
See also
Other Similarity indexes:
GOC(),
JC69_distance(),
K80_distance(),
correlation_index(),
karyotype_index(),
slidingWindow(),
strand_randomisation_index(),
synteny_index()
Examples
parameters <- readTrainFile(system.file("extdata/example.train", package = "GenomicBreaks"))
T92_distance(parameters)
#> [1] 0.01617185