Uses of Class
pal.substmodel.RateDistribution
Packages that use RateDistribution
Package
Description
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
Classes describing substitution models, i.e.
Utility classes for converting PAL objects to and from XML documents.
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Uses of RateDistribution in pal.eval
Constructors in pal.eval with parameters of type RateDistributionModifierConstructorDescriptionGeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, RateMatrix model, RateDistribution distribution) Constructor taking site pattern, tree rate matrix, and a rate distribution -
Uses of RateDistribution in pal.substmodel
Subclasses of RateDistribution in pal.substmodelModifier and TypeClassDescriptionclassdiscrete Gamma distribution (Z.classinvariable sites model (two-rate model with mean rate = 1.0)classuniform rate distributionMethods in pal.substmodel with parameters of type RateDistributionModifier and TypeMethodDescriptionstatic final SubstitutionModelSubstitutionModel.Utils.createSubstitutionModel(RateMatrix rm, RateDistribution rd) static final SubstitutionModelSubstitutionModel.Utils.createSubstitutionModel(RateMatrix rm, RateDistribution rd, boolean parameteriseDistribution) Constructors in pal.substmodel with parameters of type RateDistributionModifierConstructorDescriptionGeneralRateDistributionSubstitutionModel(NeoRateMatrix base, RateDistribution rateDistribution, DataType dt, double[] frequencies) -
Uses of RateDistribution in pal.xml
Methods in pal.xml that return RateDistributionModifier and TypeMethodDescriptionstatic RateDistributionElementParser.parseRateDistribution(Element e)