Uses of Class
pal.mep.MutationRateModel

Packages that use MutationRateModel

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

Methods in pal.coalescent with parameters of type MutationRateModel

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

Subclasses of MutationRateModel in pal.mep

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

MutationRateModel	MutationRateModel.Factory.generateNewModel() Request a new MutationRateModel instance
MutationRateModel	SteppedMutationRate.getCopy()
abstract MutationRateModel	MutationRateModel.getCopy()
MutationRateModel	ConstantMutationRate.getCopy()
MutationRateModel	WindowedMutationRate.getCopy()

Constructors in pal.mep with parameters of type MutationRateModel

MutationRateModel(MutationRateModel toCopy)

Uses of MutationRateModel in pal.supgma

Methods in pal.supgma with parameters of type MutationRateModel

static RateHandler

RateHandler.Utils.getSetRateHandler(MutationRateModel model)

Uses of MutationRateModel in pal.tree

Methods in pal.tree that return MutationRateModel

MutationRateModel

MutationRateModelTree.getMutationRateModel() returns mu

Methods in pal.tree with parameters of type MutationRateModel

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

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).

Uses of MutationRateModel in pal.xml

Methods in pal.xml that return MutationRateModel

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

static org.w3c.dom.Element

ElementFactory.createMutationRateModelElement(MutationRateModel muModel, org.w3c.dom.Document document) Creates an XML element representing a mutation rate model.