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Packages that use NeoRateMatrix | |
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pal.substmodel | Classes describing substitution models, i.e. |
Uses of NeoRateMatrix in pal.substmodel |
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Classes in pal.substmodel that implement NeoRateMatrix | |
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class |
GeneralPoissonRateMatrix
A general rate matrix class for JC69/F81 style rate matrices (but for all data types) |
class |
GeneralREVRateMatrix
A general rate matrix class for REV style rate matrices (GTR but for all data types) Includes the ability for arbitarily constraints |
Methods in pal.substmodel with parameters of type NeoRateMatrix | |
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static SubstitutionModel |
SubstitutionModel.Utils.createSubstitutionModel(NeoRateMatrix rm,
DataType dt,
double[] equilibriumFrequencies)
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Constructors in pal.substmodel with parameters of type NeoRateMatrix | |
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GeneralRateDistributionSubstitutionModel(NeoRateMatrix base,
RateDistribution rateDistribution,
DataType dt,
double[] frequencies)
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MultiRateMatrixHandler(NeoRateMatrix[] rateMatrices,
double[] equilibriumFrequencies,
double[] initialClassProportions)
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RateMatrixHandler(NeoRateMatrix rateMatrix,
double[] equilibriumFrequencies)
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SimpleRateMatrixGroup(NeoRateMatrix[] baseMatrices,
double[] equilibriumFrequencies,
double[] initialClassProbabilities,
DataType dataType)
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SingleClassSubstitutionModel(NeoRateMatrix base,
DataType dt,
double[] frequencies)
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