public static class SubstitutionModel.Utils
extends java.lang.Object
Constructor | Description |
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Utils() |
Modifier and Type | Method | Description |
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static SubstitutionModel |
createSubstitutionModel(NeoRateMatrix rm,
DataType dt,
double[] equilibriumFrequencies) |
|
static SubstitutionModel |
createSubstitutionModel(RateMatrix rm) |
|
static SubstitutionModel |
createSubstitutionModel(RateMatrix rm,
RateDistribution rd) |
|
static SubstitutionModel |
createSubstitutionModel(RateMatrix rm,
RateDistribution rd,
boolean parameteriseDistribution) |
|
static double[][][] |
generateTransitionProbabilityTables(SubstitutionModel model) |
public static final double[][][] generateTransitionProbabilityTables(SubstitutionModel model)
public static final SubstitutionModel createSubstitutionModel(RateMatrix rm)
public static final SubstitutionModel createSubstitutionModel(NeoRateMatrix rm, DataType dt, double[] equilibriumFrequencies)
public static final SubstitutionModel createSubstitutionModel(RateMatrix rm, RateDistribution rd)
public static final SubstitutionModel createSubstitutionModel(RateMatrix rm, RateDistribution rd, boolean parameteriseDistribution)
parameteriseDistribution
- If true will include the distribution parameters as part of the
substitution modle parameters, if false then the distribution parameters are set from the
point of view of the substitution model.