The Tamura–Nei 1993 (TN93) distance extends the T92 distance by allowing unequal base frequencies and two distinct transition components, plus transversions.
Arguments
- m
A matrix of counts or probabilities for bases of the target genome aligned to bases on the query genome. As a convenience it can also receive a list produced by the
readTrainFile()function, containing this matrix.
Value
Returns a numeric value show the evolutionary distance between two genomes. the larger the value, the more different the two genomes are.
Details
Let \(P_R\) be the fraction of purine transitions (A↔G), \(P_Y\) the fraction of pyrimidine transitions (C↔T), and \(Q\) the fraction of transversions among A/C/G/T pairs. Let \(\pi_A, \pi_C, \pi_G, \pi_T\) be the average base frequencies across the two sequences (row and column marginals averaged), \(\pi_R = \pi_A + \pi_G\), and \(\pi_Y = \pi_C + \pi_T\).
The TN93 distance is: $$ d_{\mathrm{TN93}} = -\,2 \pi_A \pi_G \, \ln\!\left(1 - \frac{P_R}{2 \pi_A \pi_G}\right) -\,2 \pi_C \pi_T \, \ln\!\left(1 - \frac{P_Y}{2 \pi_C \pi_T}\right) -\,2 \pi_R \pi_Y \, \ln\!\left(1 - \frac{Q}{2 \pi_R \pi_Y}\right) $$ v
References
Tamura, K. and Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10:512–26. doi:10.1093/oxfordjournals.molbev.a040023
See also
Other Alignment statistics:
F81_distance(),
GCequilibrium(),
GCpressure(),
GCproportion(),
HKY85_distance(),
JC69_distance(),
K80_distance(),
P_distance(),
T92_distance(),
exampleSubstitutionMatrix,
gapProportion(),
logDet_distance()
Other Similarity indexes:
F81_distance(),
GOC(),
HKY85_distance(),
JC69_distance(),
K80_distance(),
P_distance(),
T92_distance(),
correlation_index(),
karyotype_index(),
logDet_distance(),
slidingWindow(),
strand_randomisation_index(),
synteny_index(),
tau_index()