- 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