Uses of Class
pal.mep.MutationRateModel
Packages that use MutationRateModel
Package
Description
Classes to model population genetic processes using the coalescent.
Classes for the analysis of "measurably evolving populations" (mep).
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
Utility classes for converting PAL objects to and from XML documents.
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Uses of MutationRateModel in pal.coalescent
Methods in pal.coalescent with parameters of type MutationRateModelModifier and TypeMethodDescriptionstatic CoalescentIntervals
IntervalsExtractor.extractFromTree
(Tree tree, MutationRateModel muModel) extracts intervals in generation times from serial clock tree (in mutation times) after taking into account mutation rate model. -
Uses of MutationRateModel in pal.mep
Subclasses of MutationRateModel in pal.mepModifier and TypeClassDescriptionclass
This class models a constant mutation rate (parameter: mu = mutation rate).class
This class models a step-wise mutation rate.class
This class models a windowed mutation rate (parameter: mu = mutation rate).Methods in pal.mep that return MutationRateModelModifier and TypeMethodDescriptionMutationRateModel.Factory.generateNewModel()
Request a new MutationRateModel instanceConstantMutationRate.getCopy()
abstract MutationRateModel
MutationRateModel.getCopy()
SteppedMutationRate.getCopy()
WindowedMutationRate.getCopy()
Constructors in pal.mep with parameters of type MutationRateModel -
Uses of MutationRateModel in pal.supgma
Methods in pal.supgma with parameters of type MutationRateModelModifier and TypeMethodDescriptionstatic final RateHandler
RateHandler.Utils.getSetRateHandler
(MutationRateModel model) -
Uses of MutationRateModel in pal.tree
Methods in pal.tree that return MutationRateModelMethods in pal.tree with parameters of type MutationRateModelModifier and TypeMethodDescriptionstatic Tree
TreeUtils.generationsToMutations
(Tree generationTree, MutationRateModel muModel) Takes a tree (in generation units) and returns a scaled version of it (in mutation units).static Tree
TreeUtils.generationsToMutations
(Tree generationTree, MutationRateModel muModel, double generationTime) Takes a tree (in generation units) and returns a scaled version of it (in mutation units).static Tree
TreeUtils.getScaled
(Tree mutationRateTree, MutationRateModel muModel) Takes a tree and returns a scaled version of it.static Tree
TreeUtils.getScaled
(Tree mutationRateTree, MutationRateModel muModel, int newUnits) Takes a tree and returns a scaled version of it.static Tree
TreeUtils.mutationsToGenerations
(Tree mutationTree, MutationRateModel muModel) Takes a tree (in mutation units) and returns a scaled version of it (in generation units).static Tree
TreeUtils.scale
(Tree mutationRateTree, MutationRateModel muModel) Deprecated.use getScaled()static Tree
TreeUtils.scale
(Tree mutationRateTree, MutationRateModel muModel, int newUnits) Deprecated.use getScaled()Constructors in pal.tree with parameters of type MutationRateModelModifierConstructorDescriptionMutationRateModelTree
(Tree t, TimeOrderCharacterData tocd, MutationRateModel model) take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).MutationRateModelTree
(Tree t, TimeOrderCharacterData tocd, MutationRateModel model, boolean includeModelParameters) take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node). -
Uses of MutationRateModel in pal.xml
Methods in pal.xml that return MutationRateModelModifier and TypeMethodDescriptionstatic MutationRateModel
ElementParser.parseMutationRateModel
(Element e) Reads a mutation rate model from a DOM Document element.Methods in pal.xml with parameters of type MutationRateModelModifier and TypeMethodDescriptionstatic Element
ElementFactory.createMutationRateModelElement
(MutationRateModel muModel, Document document) Creates an XML element representing a mutation rate model.