Uses of Class
pal.misc.PalObjectListener.EventGenerator
Packages that use PalObjectListener.EventGenerator
Package
Description
Classes that don't fit elsewhere ;^)
Classes describing substitution models, i.e.
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Uses of PalObjectListener.EventGenerator in pal.misc
Subclasses of PalObjectListener.EventGenerator in pal.miscModifier and TypeClassDescriptionstatic classA Utility class for using as the superclass to subclasses which are based on double arraysstatic classA 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
Subclasses of PalObjectListener.EventGenerator in pal.substmodelModifier and TypeClassDescriptionclassdiscrete Gamma distribution (Z.classclassinvariable sites model (two-rate model with mean rate = 1.0)classabstract base class for models of rate variation over sites employing a discrete rate distributionclassclassuniform rate distributionstatic classA 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 classA 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.