Uses of Class
pal.substmodel.RateDistribution
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Packages that use RateDistribution Package Description pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.pal.substmodel Classes describing substitution models, i.e.pal.xml 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 RateDistribution Constructor Description GeneralLikelihoodCalculator(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.substmodel Modifier and Type Class Description class
GammaRates
discrete Gamma distribution (Z.class
InvariableSites
invariable sites model (two-rate model with mean rate = 1.0)class
UniformRate
uniform rate distributionMethods in pal.substmodel with parameters of type RateDistribution Modifier and Type Method Description static SubstitutionModel
SubstitutionModel.Utils. createSubstitutionModel(RateMatrix rm, RateDistribution rd)
static SubstitutionModel
SubstitutionModel.Utils. createSubstitutionModel(RateMatrix rm, RateDistribution rd, boolean parameteriseDistribution)
Constructors in pal.substmodel with parameters of type RateDistribution Constructor Description GeneralRateDistributionSubstitutionModel(NeoRateMatrix base, RateDistribution rateDistribution, DataType dt, double[] frequencies)
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Uses of RateDistribution in pal.xml
Methods in pal.xml that return RateDistribution Modifier and Type Method Description static RateDistribution
ElementParser. parseRateDistribution(org.w3c.dom.Element e)
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