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D

data - Variable in class Alignments.Alignment
The list of sites in the alignment
det() - Method in class Maths.LUDecomposition
Determinant
Distributions - Class in Models
Class to calculate stationary and quasi-stationary distributions
Distributions() - Constructor for class Models.Distributions
 
Distributions.Calculation - Enum in Models
Enumeration of the different methods of calculating a distribution
Distributions.DistributionsException - Exception in Models
Exception for use there is a problem calculating a distribution
Distributions.DistributionsException(String) - Constructor for exception Models.Distributions.DistributionsException
Default constructor
divide(SquareMatrix) - Method in class Maths.SquareMatrix
Divides this matrix by another (this / B) and returns a new matrix as the result
DNAModelFactory - Class in Models
A factory for easing the creation of many standard DNA models
DuplicationAlignment - Class in Alignments
Represents a duplication "alignment" - a set of gene families with their associated size in each species
DuplicationAlignment(File) - Constructor for class Alignments.DuplicationAlignment
Creates a duplication alignment from a file.
DuplicationAlignment(File, Ambiguous) - Constructor for class Alignments.DuplicationAlignment
Creates a duplication alignment which contains ambiguous data.
DuplicationModelFactory - Class in Models
A factory for easing the creation of some simple gene-family models
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