gtr(Double[] rates, Double[] freq, Number meanRate)

The GTR instantaneous rate matrix. Takes relative rates and base frequencies and produces an GTR rate matrix.

Parameters

  • Double[] rates - the relative rates of the GTR process.
  • Double[] freq - the base frequencies.
  • Number meanRate - (optional) the rate of substitution.

Return type

Double[][]

Examples

  • gtrCoalescent.lphy

Reference

Tavaré, S. (1986). Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on mathematics in the life sciences, 17(2), 57-86.