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taxa
- Variable in class Alignments.
Alignment
The list of taxa in the alignment
test(Tree, Alignment, Alignment, Parameters, Parameters)
- Method in class Simulations.
HypothesisTest
Does a hpyothesis test on the given data and gives a p-value
test(Tree, Alignment, Alignment, Parameters, Parameters, Map<String, String>)
- Method in class Simulations.
HypothesisTest
Does a hpyothesis test on the given data and gives a p-value
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.
Alignment.UniqueSite
toString()
- Method in class Alignments.
Site
toString()
- Method in exception Exceptions.
GeneralException
toString()
- Method in class Likelihood.
Likelihood.NodeLikelihood
toString()
- Method in class Likelihood.
Likelihood.RateLikelihood
toString()
- Method in class Likelihood.
Likelihood.SiteLikelihood
toString()
- Method in class Likelihood.
Likelihood
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
toString()
- Method in class Utils.
ToDoubleHashMap
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
TreeFigure
- Class in
Trees
Class for visualising trees.
TreeFigure(Tree)
- Constructor for class Trees.
TreeFigure
Constructor
Trees
- package Trees
Provides classes to define a tree and any constraints on that tree.
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