Uses of Class
Trees.Tree

Packages that use Tree

Package	Description
Alignments	Provides class for dealing with "alignments" and the sites in an alignment.
Ancestors	Provides classed to calculate ancestral reconstruction.
Likelihood	Provides classes for calculating the likelihood of a tree given a model and an alignment.
ModelTest
Simulations	Provides a class to create simulated data.
Trees	Provides classes to define a tree.

Uses of Tree in Alignments

Methods in Alignments with parameters of type Tree

Modifier and Type	Method and Description
java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood>	Site.getInitialNodeLikelihoods(Tree t, java.util.Map<java.lang.String,java.lang.Integer> map) Gets initial node likelihoods based on the site and tree.

Uses of Tree in Ancestors

Methods in Ancestors with parameters of type Tree

Modifier and Type	Method and Description
java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood>	Assignment.getInitialNodeLikelihoods(Tree t, Site s, java.util.Map<java.lang.String,java.lang.Integer> map) Creates initial node likelihoods using this assignment.
static AncestralJoint	AncestralJoint.newInstance(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t) Returns an object of this class that can be used for joint reconstruction.
static AncestralMarginal	AncestralMarginal.newInstance(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t) Returns an object of this class that can be used for marginal reconstruction.
static AncestralJoint	AncestralJoint.newInstance(Model m, Alignment a, Tree t) Returns an object of this class that can be used for joint reconstruction.
static AncestralMarginal	AncestralMarginal.newInstance(Model m, Alignment a, Tree t) Returns an object of this class that can be used for marginal reconstruction.

Method parameters in Ancestors with type arguments of type Tree

Modifier and Type	Method and Description
static AncestralJoint	AncestralJoint.newInstance(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t) Returns an object of this class that can be used for joint reconstruction.
static AncestralJoint	AncestralJoint.newInstance(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t) Returns an object of this class that can be used for joint reconstruction.

Constructors in Ancestors with parameters of type Tree

Constructor and Description
AncestralMarginal(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t) Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment and a tree.
AncestralMarginal(Model m, Alignment a, Tree t) Creates an object to calculate an ancestral reconstruction for a given model, alignment and tree

Constructor parameters in Ancestors with type arguments of type Tree

Constructor and Description
AncestralMarginal(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment and a tree.
AncestralMarginal(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates an object to calculate an ancestral reconstruction for a given model, alignment and tree

Uses of Tree in Likelihood

Fields in Likelihood with type parameters of type Tree

Modifier and Type	Field and Description
protected java.util.Map<java.lang.String,Tree>	Calculator.t The tree to do the calculation on.

Methods in Likelihood with parameters of type Tree

Modifier and Type	Method and Description
abstract SiteLikelihood	Calculator.calculateSite(Site s, Tree t, Parameters p, Probabilities tp, java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> nl) Calculate the likelihood for a single site.
SiteLikelihood	StandardCalculator.calculateSite(Site s, Tree t, Parameters p, Probabilities tp, java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> nl)

Constructors in Likelihood with parameters of type Tree

Constructor and Description
Calculator.SiteCalculator(Site s, Tree t, Parameters p, Probabilities tp, java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> nl) Standard constructor
Probabilities(Model m, Tree t, Parameters p) Constructor
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t, Alignment unobserved) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(Model m, Alignment a, Tree t) Creates an object to calculate the likelihood for a given model, alignment and tree.
StandardCalculator(Model m, Alignment a, Tree t, Alignment unobserved) Creates a class to calculate the likelihood for a given model, alignment, tree and missing data

Constructor parameters in Likelihood with type arguments of type Tree

Constructor and Description
Calculator(java.util.Map<java.lang.String,Model> m, java.util.Map<java.lang.String,Tree> t, java.util.HashMap<Site,java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood>> snl) Default constructor.
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t, Alignment unobserved) Creates a class to calculate the likelihood for a given set of models, an alignment, a tree and unobserved data.
StandardCalculator(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t, Alignment unobserved) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.

Uses of Tree in ModelTest

Methods in ModelTest with parameters of type Tree

Modifier and Type	Method and Description
double	HypothesisTest.test(Tree t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams) Does a hypothesis test on the given data and gives a p-value
double	HypothesisTest.test(Tree t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams, java.util.Map<java.lang.String,java.lang.String> recode) Does a hypothesis test on the given data and gives a p-value

Method parameters in ModelTest with type arguments of type Tree

Modifier and Type	Method and Description
double	HypothesisTest.test(java.util.Map<java.lang.String,Tree> t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams) Does a hypothesis test on the given data and gives a p-value
double	HypothesisTest.test(java.util.Map<java.lang.String,Tree> t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams, java.util.Map<java.lang.String,java.lang.String> recode) Does a hypothesis test on the given data and gives a p-value

Uses of Tree in Simulations

Constructors in Simulations with parameters of type Tree

Constructor and Description
Simulate(java.util.Map<java.lang.String,Model> m, Tree t, Parameters p) Creates an object to simulate data for a given set of models, a tree and parameters.
Simulate(java.util.Map<java.lang.String,Model> m, Tree t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given set of models, a tree, parameters and unobserved states.
Simulate(Model m, Tree t, Parameters p) Creates an object to simulate data for a given model, tree and parameters.
Simulate(Model m, Tree t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given model, tree, parameters and unobserved states.

Constructor parameters in Simulations with type arguments of type Tree

Constructor and Description
Simulate(java.util.Map<java.lang.String,Model> m, java.util.Map<java.lang.String,Tree> t, Parameters p) Creates an object to simulate data for a given set of models and trees, parameters and unobserved states.
Simulate(java.util.Map<java.lang.String,Model> m, java.util.Map<java.lang.String,Tree> t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given set of models and trees, parameters and unobserved states.
Simulate(Model m, java.util.Map<java.lang.String,Tree> t, Parameters p) Creates an object to simulate data for a given model, set of trees, parameters and unobserved states.
Simulate(Model m, java.util.Map<java.lang.String,Tree> t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given model, set of trees, parameters and unobserved states.

Uses of Tree in Trees

Methods in Trees that return Tree

Modifier and Type	Method and Description
static Tree	Tree.fromFile(java.io.File f) Creates a tree from a file containing a Newick string
static Tree	Tree.fromNewickString(java.lang.String newick) Creates a tree from a newick string
Tree	Tree.midPointRoot(java.lang.String newRootName) Mid point roots the tree and returns a new tree
static Tree	Tree.randomTree(java.util.List<java.lang.String> taxa, boolean rooted) Creates a random rooted or unrooted tree from a list of taxa
Tree	Tree.scaledTo(double length) Returns a new tree where the lengths are scales so the total length is different

Methods in Trees with parameters of type Tree

Modifier and Type	Method and Description
double	Tree.branchScore(Tree t) Calculates the branch score distance between this tree and another tree
int	Tree.RF(Tree t) Calculates the RF distance between this tree and another tree
double	Tree.weightedRF(Tree t) Calculates the weighted (by branch length) RF distance between this tree and another tree

Constructors in Trees with parameters of type Tree

Constructor and Description
Tree(Tree old, Parameters p) Duplicates a tree topology while replacing branch lengths using the appropriate parameter
TreeFigure(Tree t) Constructor