The P-distance is simply the percentage of the aligned base pairs where the two bases are different. See May 2004 for a discussion on the many ways to compute percent identity (and therefore difference.)
Arguments
- train_parameters
A list containing the probabilities of the alignment, produced by the
readTrainFile()function.
Value
A numeric value representing the evolutionary distance between two genomes. The larger the value, the more divergent the genomes.
References
May, A. C. W. (2004). Percent Sequence Identity: The Need to Be Explicit. Structure, 12(5), 737–738. doi:doi.org/10.1016/j.str.2004.04.001
See also
Other Similarity indexes:
F81_distance(),
GOC(),
JC69_distance(),
K80_distance(),
T92_distance(),
correlation_index(),
karyotype_index(),
slidingWindow(),
strand_randomisation_index(),
synteny_index()
Examples
parameters <- readTrainFile(system.file("extdata/example.train", package = "GenomicBreaks"))
P_distance(parameters)
#> [1] 0.015976