- 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.