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Packages that use PalObjectListener.EventGenerator | |
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pal.misc | Classes that don't fit elsewhere ;^) |
pal.substmodel | Classes describing substitution models, i.e. |
Uses of PalObjectListener.EventGenerator in pal.misc |
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Subclasses of PalObjectListener.EventGenerator in pal.misc | |
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static class |
Parameterized.ParameterizedBase
A Utility class for using as the superclass to subclasses which are based on double arrays |
static class |
Parameterized.ParameterizedUser
A Utility class for using as the superclass to subclasses which work by adding functionality to a general Parameterized object (the base Parameterized object) |
Uses of PalObjectListener.EventGenerator in pal.substmodel |
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Subclasses of PalObjectListener.EventGenerator in pal.substmodel | |
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class |
GammaRates
discrete Gamma distribution (Z. |
class |
GeneralRateDistributionSubstitutionModel
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class |
InvariableSites
invariable sites model (two-rate model with mean rate = 1.0) |
class |
RateDistribution
abstract base class for models of rate variation over sites employing a discrete rate distribution |
class |
SingleClassSubstitutionModel
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class |
UniformRate
uniform rate distribution |
static class |
YangCodonModel.SimpleNeutralSelection
A Substitution Model which can be used to implment the Neutral Model (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of trwo base YangCodon models where omega=0, omega=1 repectively [1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene. |
static class |
YangCodonModel.SimplePositiveSelection
A Substitution Model which can be used to implment the Postitive Selection (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of a three base Codon model where omega=0, omega=1 and omega=free [1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene. |
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