Package | Description |
---|---|
pal.coalescent |
Classes to model population genetic processes using the coalescent.
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pal.mep |
Classes for the analysis of "measurably evolving populations" (mep).
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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.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Class and Description |
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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).
|
Modifier and Type | Method and Description |
---|---|
MutationRateModel |
MutationRateModel.Factory.generateNewModel()
Request a new MutationRateModel instance
|
MutationRateModel |
SteppedMutationRate.getCopy() |
abstract MutationRateModel |
MutationRateModel.getCopy() |
MutationRateModel |
WindowedMutationRate.getCopy() |
MutationRateModel |
ConstantMutationRate.getCopy() |
Constructor and Description |
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MutationRateModel(MutationRateModel toCopy) |
Modifier and Type | Method and Description |
---|---|
static RateHandler |
RateHandler.Utils.getSetRateHandler(MutationRateModel model) |
Modifier and Type | Method and Description |
---|---|
MutationRateModel |
MutationRateModelTree.getMutationRateModel()
returns mu
|
Modifier and Type | Method and Description |
---|---|
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()
|
Constructor and Description |
---|
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).
|
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).
|
Modifier and Type | Method and Description |
---|---|
static MutationRateModel |
ElementParser.parseMutationRateModel(org.w3c.dom.Element e)
Reads a mutation rate model from a DOM Document element.
|
Modifier and Type | Method and Description |
---|---|
static org.w3c.dom.Element |
ElementFactory.createMutationRateModelElement(MutationRateModel muModel,
org.w3c.dom.Document document)
Creates an XML element representing a mutation rate model.
|