Uses of Class
Alignments.Alignment

Packages that use Alignment
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. 
 

Uses of Alignment in Alignments
 

Subclasses of Alignment in Alignments
 class DuplicationAlignment
          Represents a duplication "alignment" - a set of gene families with their associated size in each species
 class SequenceAlignment
          Represents a sequence alignment
 

Methods in Alignments that return Alignment
 Alignment Alignment.recode(java.util.Map<java.lang.String,java.lang.String> recode)
          Recodes the alignment and returns it
 

Methods in Alignments with parameters of type Alignment
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).
 

Uses of Alignment in Ancestors
 

Methods in Ancestors that return Alignment
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
 

Methods in Ancestors with parameters of type Alignment
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 Alignment
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
 

Uses of Alignment in Likelihood
 

Constructors in Likelihood with parameters of type Alignment
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
 

Uses of Alignment in Simulations
 

Methods in Simulations that return Alignment
 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.
 

Constructors in Simulations with parameters of type Alignment
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.