Package | Description |
---|---|
Ancestors |
Provides classed to calculate ancestral reconstruction.
|
Constraints |
Provides classes to constrain the state of internal nodes.
|
Likelihood |
Provides classes for calculating the likelihood of a tree given a model and
an alignment.
|
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 |
---|---|
static AncestralJoint |
AncestralJoint.newInstance(Model m,
Alignment a,
Tree t)
Returns an object of this class that can be used for joint reconstruction.
|
Constructor and Description |
---|
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
|
Modifier and Type | Method and Description |
---|---|
SiteConstraints |
Constrainer.getConstraints(Tree t,
Site s)
Gets the consraints on an the external nodes of a site given the tree
and the state of the leafs.
|
SiteConstraints |
NoConstraints.getConstraints(Tree t,
Site s) |
Constructor and Description |
---|
Calculator.SiteCalculator(Site s,
Tree t,
SiteConstraints con,
Probabilities tp)
Standard constructor
|
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
|
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 |
---|---|
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
|
Tree |
Tree.scaledTo(double length)
Returns a new tree where the lengths are scales so the total length is
different
|
Constructor and Description |
---|
Tree(Tree old,
Parameters p)
Duplicates a tree topology while replacing branch lengths using
the appropiate parameter
|