Uses of Class
Trees.Tree

Packages that use Tree
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. 
 

Uses of Tree in Ancestors
 

Methods in Ancestors with parameters of type Tree
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 Tree
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 Tree in Constraints
 

Methods in Constraints with parameters of type Tree
 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)
           
 

Uses of Tree in Likelihood
 

Constructors in Likelihood with parameters of type Tree
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
 

Uses of Tree in Simulations
 

Constructors in Simulations with parameters of type Tree
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.
 

Uses of Tree in Trees
 

Methods in Trees that return Tree
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
 

Constructors in Trees with parameters of type Tree
Tree(Tree old, Parameters p)
          Duplicates a tree topology while replacing branch lengths using the appropiate parameter