nucleotideModel(BModelSet modelSet, Integer modelIndicator, Double[] rates, Double[] freq, Number meanRate)

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

Parameters

  • BModelSet modelSet - The set of models to choose from. Valid value are: allreversible, transitionTransversionSplit, namedSimple, namedExtended.
  • Integer modelIndicator - the index of the model to be employed
  • 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

  • simpleBModelTest.lphy
  • simpleBModelTest2.lphy

Reference

Bouckaert, R., Drummond, A. bModelTest: Bayesian phylogenetic site model averaging and model comparison. BMC Evol Biol 17, 42 (2017). https://doi.org/10.1186/s12862-017-0890-6https://doi.org/10.1186/s12862-017-0890-6