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