Package | Description |
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pal.substmodel |
Classes describing substitution models, i.e.
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Modifier and Type | Class and Description |
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class |
GeneralPoissonRateMatrix
A general rate matrix class for JC69/F81 style rate matrices (but for all data types)
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class |
GeneralREVRateMatrix
A general rate matrix class for REV style rate matrices (GTR but for all data types)
Includes the ability for arbitarily constraints
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Modifier and Type | Method and Description |
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static SubstitutionModel |
SubstitutionModel.Utils.createSubstitutionModel(NeoRateMatrix rm,
DataType dt,
double[] equilibriumFrequencies) |
Constructor and Description |
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GeneralRateDistributionSubstitutionModel(NeoRateMatrix base,
RateDistribution rateDistribution,
DataType dt,
double[] frequencies) |
MultiRateMatrixHandler(NeoRateMatrix[] rateMatrices,
double[] equilibriumFrequencies,
double[] initialClassProportions) |
RateMatrixHandler(NeoRateMatrix rateMatrix,
double[] equilibriumFrequencies) |
SimpleRateMatrixGroup(NeoRateMatrix[] baseMatrices,
double[] equilibriumFrequencies,
double[] initialClassProbabilities,
DataType dataType) |
SingleClassSubstitutionModel(NeoRateMatrix base,
DataType dt,
double[] frequencies) |