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Packages that use MutationRateModel | |
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pal.coalescent | Classes to model population genetic processes using the coalescent. |
pal.mep | Classes for the analysis of "measurably evolving populations" (mep). |
pal.supgma | |
pal.tree | Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint). |
pal.xml | Utility classes for converting PAL objects to and from XML documents. |
Uses of MutationRateModel in pal.coalescent |
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Methods in pal.coalescent with parameters of type MutationRateModel | |
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static 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 |
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Subclasses of MutationRateModel in pal.mep | |
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class |
ConstantMutationRate
This class models a constant mutation rate (parameter: mu = mutation rate). |
class |
SteppedMutationRate
This class models a step-wise mutation rate. |
class |
WindowedMutationRate
This class models a windowed mutation rate (parameter: mu = mutation rate). |
Methods in pal.mep that return MutationRateModel | |
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MutationRateModel |
MutationRateModel.Factory.generateNewModel()
Request a new MutationRateModel instance |
MutationRateModel |
SteppedMutationRate.getCopy()
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abstract MutationRateModel |
MutationRateModel.getCopy()
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MutationRateModel |
ConstantMutationRate.getCopy()
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MutationRateModel |
WindowedMutationRate.getCopy()
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Constructors in pal.mep with parameters of type MutationRateModel | |
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MutationRateModel(MutationRateModel toCopy)
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Uses of MutationRateModel in pal.supgma |
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Methods in pal.supgma with parameters of type MutationRateModel | |
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static RateHandler |
RateHandler.Utils.getSetRateHandler(MutationRateModel model)
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Uses of MutationRateModel in pal.tree |
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Methods in pal.tree that return MutationRateModel | |
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MutationRateModel |
MutationRateModelTree.getMutationRateModel()
returns mu |
Methods in pal.tree with parameters of type MutationRateModel | |
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static 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 MutationRateModel | |
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MutationRateModelTree(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). |
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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 |
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Methods in pal.xml that return MutationRateModel | |
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static MutationRateModel |
ElementParser.parseMutationRateModel(org.w3c.dom.Element e)
Reads a mutation rate model from a DOM Document element. |
Methods in pal.xml with parameters of type MutationRateModel | |
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static org.w3c.dom.Element |
ElementFactory.createMutationRateModelElement(MutationRateModel muModel,
org.w3c.dom.Document document)
Creates an XML element representing a mutation rate model. |
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