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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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