hky(Number kappa, Double[] freq, Number meanRate)

The HKY instantaneous rate matrix. Takes a kappa and base frequencies (and optionally a total rate) and produces an HKY85 rate matrix.

Parameters

  • Number kappa - the kappa of the HKY process.
  • Double[] freq - the base frequencies.
  • Number meanRate - (optional) the total rate of substitution per unit time. Default 1.0.

Return type

Double[][]

Examples

  • hkyCoalescent.lphy

Reference

Hasegawa, M., Kishino, H. & Yano, T. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22, 160–174https://doi.org/10.1007/BF02101694