Package | Description |
---|---|
Alignments |
Provides class for dealing with "alignments" and the sites in an alignment.
|
Ancestors |
Provides classed to calculate ancestral reconstruction.
|
Likelihood |
Provides classes for calculating the likelihood of a tree given a model and
an alignment.
|
Simulations |
Provides a class to create simulate data.
|
Modifier and Type | Class and Description |
---|---|
class |
DuplicationAlignment
Represents a duplication "alignment" - a set of gene families with their
associated size in each species
|
class |
SequenceAlignment
Represents a sequence alignment
|
Modifier and Type | Method and Description |
---|---|
Alignment |
Alignment.recode(java.util.Map<java.lang.String,java.lang.String> recode)
Recodes the alignment and returns it
|
Modifier and Type | Method and Description |
---|---|
static void |
DuplicationAlignment.writeFile(Alignment a,
java.io.File f)
Writes a alignment to a file in the duplication alignment format described
above.
|
static void |
SequenceAlignment.writeFile(Alignment a,
java.io.File f)
Writes a alignment to a file in the format described in
SequenceAlignment.SequenceAlignment(java.io.File) . |
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) |
Alignment |
AncestralMarginal.Result.getAlignment()
Gets the reconstructed alignment
|
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
|
Constructor and Description |
---|
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
|
Modifier and Type | Method and Description |
---|---|
Alignment |
Simulate.getAlignment(int length)
Gets a simulated alignment, not returing the state of internal nodes
|
Alignment |
Simulate.getAlignment(int length,
boolean internal)
Gets a simulated alignment
|
Alignment |
Simulate.getAlignment(int length,
boolean internal,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment.
|
Alignment |
Simulate.getAlignment(int length,
java.util.Map<java.lang.String,java.lang.String> recode)
Gets a simulated alignment, not returing the state of internal nodes.
|
Constructor and Description |
---|
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.
|