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.
|
Constructor and Description |
---|
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 | Class and Description |
---|---|
class |
NoConstraints
Simple implementation of
Constrainer that imposes no constraints |
Constructor and Description |
---|
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
|
Constructor and Description |
---|
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.
|