Uses of Interface
pal.substmodel.NeoRateMatrix

Packages that use NeoRateMatrix

pal.substmodel

Classes describing substitution models, i.e.

Uses of NeoRateMatrix in pal.substmodel

Classes in pal.substmodel that implement NeoRateMatrix

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

static SubstitutionModel

SubstitutionModel.Utils.createSubstitutionModel(NeoRateMatrix rm, DataType dt, double[] equilibriumFrequencies)

Constructors in pal.substmodel with parameters of type NeoRateMatrix

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)