Uses of Class
Models.Model

Packages that use Model

Package	Description
Ancestors	Provides classed to calculate ancestral reconstruction.
Likelihood	Provides classes for calculating the likelihood of a tree given a model and an alignment.
Models	Provides classes for defining a phylogenetic model.
ModelTest
Simulations	Provides a class to create simulated data.

Uses of Model in Ancestors

Methods in Ancestors with parameters of type Model

Modifier and Type	Method and Description
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.
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 Model

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(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.

Constructors in Ancestors with parameters of type Model

Constructor and Description
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
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 Model

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(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.

Uses of Model in Likelihood

Fields in Likelihood with type parameters of type Model

Modifier and Type	Field and Description
protected java.util.Map<java.lang.String,Model>	Calculator.m The model to do the calculation on.

Constructors in Likelihood with parameters of type Model

Constructor and Description
Probabilities(Model m, Tree t, Parameters p) Constructor
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.
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 Model

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(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.

Uses of Model in Models

Methods in Models that return Model

Modifier and Type	Method and Description
static Model	DuplicationModelFactory.BD_NoZero_Gamma(Parameters p, int num, int numCats) Creates a Birth Death model with no zero state and gamma distributed rates-across sites.
static Model	DuplicationModelFactory.BD_NoZero_Gamma(Parameters p, int num, int numCats, boolean fixed) Creates a Birth Death model with no zero state and gamma distributed rates-across sites.
static Model	DuplicationModelFactory.BD_NoZero(Parameters p, int num) Creates a Birth Death model with no zero state.
static Model	DuplicationModelFactory.BD_NoZero(Parameters p, int num, boolean fixed) Creates a Birth Death model with no zero state.
static Model	DuplicationModelFactory.BDI_Gamma(Parameters p, int num, int numCats) Creates a simple BDI model with gamma-distributed rate across sites.
static Model	DuplicationModelFactory.BDI_Gamma(Parameters p, int num, int numCats, boolean fixed) Creates a simple BDI model with gamma-distributed rate across sites
static Model	DuplicationModelFactory.BDI(Parameters p, int num) Creates a simple BDI model.
static Model	DuplicationModelFactory.BDI(Parameters p, int num, boolean fixed) Creates a simple BDI model
static Model	DuplicationModelFactory.BDIE_Gamma(Parameters p, int num, int numCats) Creates a simple BDI model with gamma-distributed rate across sites.
static Model	DuplicationModelFactory.BDIE_Gamma(Parameters p, int num, int numCats, boolean fixed) Creates a simple BDIE model with gamma-distributed rate across sites
static Model	DuplicationModelFactory.BDIE(Parameters p, int num, boolean fixed) Creates a simple BDIE model
static Model	DNAModelFactory.Felsenstein81_Gamma(int numCats) Creates an instance of a JFelsenstein 81 model with gamma-distributed rate across sites
static Model	DNAModelFactory.Felsenstein81_Gamma(Parameters p, int numCats) Creates an instance of a JFelsenstein 81 model with gamma-distributed rate across sites
static Model	DNAModelFactory.Felsenstein81() Creates an instance of a Felsenstein 81 model
static Model	DNAModelFactory.Felsenstein81(Parameters p) Creates an instance of a Felsenstein 81 model
static Model	Model.fromFile(java.io.File f) Creates a new model from a file.
static Model	Model.gammaRates(RateCategory r, java.lang.String gamma, int cats) Creates a new model with multiple rate classes distributed by a gamma distribution (see Yang 1993) based on a single rate class
Model	DNAModelFactory.getModel() Returns a new instance of the relevant model
static Model	DNAModelFactory.GTR_Gamma(int numCats) Creates an instance of a General Time Reversible model with gamma-distributed rate across sites
static Model	DNAModelFactory.GTR_Gamma(Parameters p, int numCats) Creates an instance of a General Time Reversible model with gamma-distributed rate across sites
static Model	DNAModelFactory.GTR() Creates an instance of a General Time Reversible model
static Model	DNAModelFactory.GTR(Parameters p) Creates an instance of a General Time Reversible model
static Model	DNAModelFactory.HKY_Gamma(int numCats) Creates an instance of a HKY model with gamma-distributed rate across sites
static Model	DNAModelFactory.HKY_Gamma(Parameters p, int numCats) Creates an instance of a HKY model with gamma-distributed rate across sites
static Model	DNAModelFactory.HKY() Creates an instance of a HKY model
static Model	DNAModelFactory.HKY(Parameters p) Creates an instance of a HKY model
static Model	DNAModelFactory.JukesCantor_Gamma(int numCats) Creates an instance of a Jukes-Cantor model with gamma-distributed rate across sites
static Model	DNAModelFactory.JukesCantor_Gamma(Parameters p, int numCats) Creates an instance of a Jukes-Cantor model with gamma-distributed rate across sites
static Model	DNAModelFactory.JukesCantor() Creates an instance of a Jukes-Cantor model
static Model	DNAModelFactory.JukesCantor(Parameters p) Creates an instance of a Jukes-Cantor model
static Model	DNAModelFactory.Kimura_Gamma(int numCats) Creates an instance of a Kimura 2-parameter model with gamma-distributed rate across sites
static Model	DNAModelFactory.Kimura_Gamma(Parameters p, int numCats) Creates an instance of a Kimura 2-parameter model with gamma-distributed rate across sites
static Model	DNAModelFactory.Kimura() Creates an instance of a Kimura 2-paramter model
static Model	DNAModelFactory.Kimura(Parameters p) Creates an instance of a Kimura 2-paramter model
static Model	DuplicationModelFactory.Parsimony_Gamma(Parameters p, int num, int numCats) Creates a simple parsimony-style model with gamma-distributed rate across sites.
static Model	DuplicationModelFactory.Parsimony_Gamma(Parameters p, int num, int numCats, boolean fixed) Creates a simple parsimony-style model with gamma-distributed rate across sites
static Model	DuplicationModelFactory.Parsimony(Parameters p, int num) Creates a simple parsimony-style model
static Model	DuplicationModelFactory.Parsimony(Parameters p, int num, boolean fixed) Creates a simple parsimony-style model
static Model	RYModelFactory.RY_Gamma(int numCats) Creates an instance of a RY model with gamma-distributed rate across sites
static Model	RYModelFactory.RY_Gamma(Parameters p, int numCats) Creates an instance of a RY model with gamma-distributed rate across sites
static Model	RYModelFactory.RY() Creates an instance of a RY model
static Model	RYModelFactory.RY(Parameters p) Creates an instance of a RY model

Uses of Model in ModelTest

Constructors in ModelTest with parameters of type Model

Constructor and Description
HypothesisTest(Model nullModel, Model altModel, Optimizer o, int reps) Constructor

Constructor parameters in ModelTest with type arguments of type Model

Constructor and Description
HypothesisTest(java.util.Map<java.lang.String,Model> nullModel, java.util.Map<java.lang.String,Model> altModel, Optimizer o, int reps) Constructor
HypothesisTest(java.util.Map<java.lang.String,Model> nullModel, java.util.Map<java.lang.String,Model> altModel, Optimizer o, int reps) Constructor

Uses of Model in Simulations

Constructors in Simulations with parameters of type Model

Constructor and Description
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.
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 Model

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(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.