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B

BD_NoZero(Parameters, int) - Static method in class Models.DuplicationModelFactory
Creates a Birth Death model with no zero state.
BD_NoZero(Parameters, int, boolean) - Static method in class Models.DuplicationModelFactory
Creates a Birth Death model with no zero state.
BD_NoZero_Gamma(Parameters, int, int) - Static method in class Models.DuplicationModelFactory
Creates a Birth Death model with no zero state and gamma distributed rates-across sites.
BD_NoZero_Gamma(Parameters, int, int, boolean) - Static method in class Models.DuplicationModelFactory
Creates a Birth Death model with no zero state and gamma distributed rates-across sites.
BDI(Parameters, int) - Static method in class Models.DuplicationModelFactory
Creates a simple BDI model.
BDI(Parameters, int, boolean) - Static method in class Models.DuplicationModelFactory
Creates a simple BDI model
BDI_Gamma(Parameters, int, int) - Static method in class Models.DuplicationModelFactory
Creates a simple BDI model with gamma-distributed rate across sites.
BDI_Gamma(Parameters, int, int, boolean) - Static method in class Models.DuplicationModelFactory
Creates a simple BDI model with gamma-distributed rate across sites
BDIE(Parameters, int, boolean) - Static method in class Models.DuplicationModelFactory
Creates a simple BDIE model
BDIE_Gamma(Parameters, int, int) - Static method in class Models.DuplicationModelFactory
Creates a simple BDI model with gamma-distributed rate across sites.
BDIE_Gamma(Parameters, int, int, boolean) - Static method in class Models.DuplicationModelFactory
Creates a simple BDIE model with gamma-distributed rate across sites
BIC - Class in ModelTest
Class for computing the BIC of several test instances (where an instance is a calculator and a set of parameters.
BIC(List<TestInstance>, Optimizer) - Constructor for class ModelTest.BIC
Creates an object containing the BIC for several test instances
Branch - Class in Trees
Represents a branch in a tree
Branch(String, String) - Constructor for class Trees.Branch
Constructor for a branch of unknown length
Branch(String, String, double) - Constructor for class Trees.Branch
Constructor for a branch of known length
branchScore(Tree) - Method in class Trees.Tree
Calculates the branch score distance between this tree and another tree
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