Uses of Class
Models.Model

Packages that use Model
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 defing a phylogenetic model. 
Simulations Provides a class to create simulate data. 
 

Uses of Model in Ancestors
 

Methods in Ancestors with parameters of type Model
static AncestralJoint AncestralJoint.newInstance(Model m, Alignment a, Tree t)
          Returns an object of this class that can be used for joint reconstruction.
 

Constructors in Ancestors with parameters of type Model
AncestralMarginal(Model m, Alignment a, Tree t)
          Creates an object to calculate an ancestral reconstruction for a given model, alignment and tree
AncestralMarginal(Model m, Alignment a, Tree t, Constrainer con)
          Creates an object to calculate an ancestral reconstruction for a given model, alignment, tree and constraints
 

Uses of Model in Likelihood
 

Constructors in Likelihood with parameters of type Model
Calculator(Model m, Alignment a, Tree t)
          Creates an object to calculate the likelihood for a given model, alignment, tree.
Calculator(Model m, Alignment a, Tree t, Alignment unobserved)
          Creates a class to calculate the likelihood for a given model, alignment, tree, missing data and constraints
Calculator(Model m, Alignment a, Tree t, Alignment unobserved, Constrainer con)
          Creates a class to calculate the likelihood for a given model, alignment, tree, unobserved data and constraints
Calculator(Model m, Alignment a, Tree t, Constrainer con)
          Creates a class to calculate the likelihood for a given model, alignment, tree and constraints
Probabilities(Model m, Tree t, Parameters p)
          Constructor
 

Uses of Model in Models
 

Methods in Models that return Model
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(Parameters p, int num)
          Creates a simple BDI model
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(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
static Model DNAModelFactory.GTR_Gamma(Parameters p, int numCats)
          Creates an instance of a General Time Reversable model with gamma-distributed rate across sites
static Model DNAModelFactory.GTR(Parameters p)
          Creates an instance of a General Time Reversable model
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(Parameters p)
          Creates an instance of a HKY model
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(Parameters p)
          Creates an instance of a Jukes-Cantor model
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(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(Parameters p, int num)
          Creates a simple parsimony-style model
 

Uses of Model in Simulations
 

Constructors in Simulations with parameters of type Model
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.
Simulate(Model m, Tree t, Parameters p, Alignment unobserved, Constrainer con)
          Creates an object to simulate data for a given model, tree, parameters, unobserved states and constraints.