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Packages that use RateDistribution | |
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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. |
Uses of RateDistribution in pal.eval |
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Constructors in pal.eval with parameters of type RateDistribution | |
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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 |
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Subclasses of RateDistribution in pal.substmodel | |
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class |
GammaRates
discrete Gamma distribution (Z. |
class |
InvariableSites
invariable sites model (two-rate model with mean rate = 1.0) |
class |
UniformRate
uniform rate distribution |
Methods in pal.substmodel with parameters of type RateDistribution | |
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static SubstitutionModel |
SubstitutionModel.Utils.createSubstitutionModel(RateMatrix rm,
RateDistribution rd)
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static SubstitutionModel |
SubstitutionModel.Utils.createSubstitutionModel(RateMatrix rm,
RateDistribution rd,
boolean parameteriseDistribution)
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Constructors in pal.substmodel with parameters of type RateDistribution | |
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GeneralRateDistributionSubstitutionModel(NeoRateMatrix base,
RateDistribution rateDistribution,
DataType dt,
double[] frequencies)
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Uses of RateDistribution in pal.xml |
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Methods in pal.xml that return RateDistribution | |
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static RateDistribution |
ElementParser.parseRateDistribution(org.w3c.dom.Element e)
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