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 defing a phylogenetic model.
|
Optimizers |
Provides classes for optimising a likelihood.
|
Parameters |
Provides classes for defining parameters used in the various calculations.
|
Simulations |
Provides a class to create simulate data.
|
Trees |
Provides classes to define a tree and any constraints on that tree.
|
Modifier and Type | Method and Description |
---|---|
abstract Alignment |
AncestralJoint.calculate(Parameters params)
Calculates the reconstruction
|
Alignment |
AncestralJointBB.calculate(Parameters p) |
Alignment |
AncestralJointDP.calculate(Parameters params) |
AncestralMarginal.Result |
AncestralMarginal.calculate(Parameters params)
Calculates the reconstruction
|
Modifier and Type | Method and Description |
---|---|
Parameters |
Likelihood.getParameters()
Gets the parameters used to calculate this likelihood
|
Modifier and Type | Method and Description |
---|---|
Likelihood |
Calculator.calculate(Parameters p)
Calculates the likelihood for a given set of parameters
|
Constructor and Description |
---|
ConfidenceInterval(Calculator l,
Parameters p)
Default constructor
|
Probabilities(Model m,
Tree t,
Parameters p)
Constructor
|
Modifier and Type | Method and Description |
---|---|
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 |
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
|
void |
Model.setParameters(Parameters p)
Sets the parameters of a model to the values contained in the
Parameters data structure. |
void |
RateCategory.setParameters(Parameters p)
Updates the parameters in the RateCategory.
|
Modifier and Type | Method and Description |
---|---|
Likelihood |
GoldenSection.maximise(Calculator l,
Parameters params) |
Likelihood |
NelderMead.maximise(Calculator l,
Parameters params) |
Likelihood |
Optimizer.maximise(Calculator l,
Parameters p)
Maximises the likelihood, logging to screen.
|
Likelihood |
GoldenSection.maximise(Calculator l,
Parameters params,
java.io.File log) |
Likelihood |
NelderMead.maximise(Calculator l,
Parameters params,
java.io.File log) |
Likelihood |
Optimizer.maximise(Calculator l,
Parameters params,
java.io.File log)
Maximises the likelihood, logging to a file.
|
Modifier and Type | Method and Description |
---|---|
Parameters |
Parameters.clone() |
static Parameters |
Parameters.fromFile(java.io.File f)
Reads parameters from a file.
|
Modifier and Type | Method and Description |
---|---|
void |
Parameters.addParameters(Parameters pp)
Adds the parameters from another set of parameters
|
Constructor and Description |
---|
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.
|
Modifier and Type | Method and Description |
---|---|
Parameters |
Tree.getParameters()
Returns a Parameters object containing a parameter for each branch length.
|
Parameters |
Tree.getParametersForEstimation()
Returns a Parameters object containing a parameter for each branch length.
|
Constructor and Description |
---|
Tree(Tree old,
Parameters p)
Duplicates a tree topology while replacing branch lengths using
the appropiate parameter
|