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T

taxa - Variable in class Alignments.Alignment
The list of taxa in the alignment
TimePassed - Class in Utils
A class to check wether a set amount of time has passed.
TimePassed(int, TimeUnit) - Constructor for class Utils.TimePassed
Defcault constructor.
ToDoubleHashMap<K> - Class in Utils
A HashMap where the values are doubles.
ToDoubleHashMap() - Constructor for class Utils.ToDoubleHashMap
 
toFile(File) - Method in class Parameters.Parameters
Writes the parameter values to a file.
toFile(File, double) - Method in class Parameters.Parameters
Writes the parameter values to a file and writes a line labeled likelihood and which gives the likelihood given as input.
toFile(File) - Method in class Trees.Tree
Writes the tree to a file in Newick format.
toFile(File, boolean) - Method in class Trees.Tree
Write the tree to a file in Newick format.
toString() - Method in class Alignments.Site
 
toString() - Method in exception Exceptions.GeneralException
 
toString() - Method in class Maths.SquareMatrix
 
toString() - Method in class Models.RateCategory
 
toString() - Method in class Parameters.Parameter
 
toString() - Method in class Parameters.Parameters
 
toString() - Method in class Trees.Branch
 
toString() - Method in class Trees.Tree
 
toString(boolean) - Method in class Trees.Tree
Returns a textual representation of the tree in Newick format
toString() - Method in class Utils.SetSettings
 
transpose() - Method in class Maths.SquareMatrix
Transposes the matrix and returns a new matrix as the result
transpose(double[][]) - Static method in class Utils.Array2D
Transposes the array
Tree - Class in Trees
Represents a phylogenetic tree.
Tree(List<Branch>) - Constructor for class Trees.Tree
Creates a tree from a list of branches
Tree(Tree, Parameters) - Constructor for class Trees.Tree
Duplicates a tree topology while replacing branch lengths using the appropiate parameter
TreeException - Exception in Trees
Exception thrown when there is a problem with a tree
TreeException(String) - Constructor for exception Trees.TreeException
Default constructor
Trees - package Trees
Provides classes to define a tree and any constraints on that tree.
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