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Packages that use Model | |
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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 |
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Methods in Ancestors with parameters of type Model | |
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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 | |
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AncestralMarginal(Model m,
Alignment a,
Tree t)
Creates an object to calculate an ancestral reconstruction for a given model, alignment and tree |
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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 |
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Constructors in Likelihood with parameters of type Model | |
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Calculator(Model m,
Alignment a,
Tree t)
Creates an object to calculate the likelihood for a given model, alignment, tree. |
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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 |
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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 |
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Calculator(Model m,
Alignment a,
Tree t,
Constrainer con)
Creates a class to calculate the likelihood for a given model, alignment, tree and constraints |
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Probabilities(Model m,
Tree t,
Parameters p)
Constructor |
Uses of Model in Models |
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Methods in Models that return Model | |
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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 |
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Constructors in Simulations with parameters of type Model | |
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Simulate(Model m,
Tree t,
Parameters p)
Creates an object to simulate data for a given model, tree and parameters. |
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Simulate(Model m,
Tree t,
Parameters p,
Alignment unobserved)
Creates an object to simulate data for a given model, tree, parameters and unobserved states. |
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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. |
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