- m - Variable in class Likelihood.Calculator
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The model to do the calculation on.
- main(String[]) - Static method in class Executable.GeLL
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Main function
- Maths - package Maths
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Provides maths classes.
- MathsParse - Class in Maths
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Class used to parse an equation represented by a string and return the result.
- MathsParse(FunctionParser...) - Constructor for class Maths.MathsParse
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Default constructor.
- maximise(Optimizable<R>, Parameters) - Method in class Optimizers.ConjugateGradient
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- maximise(Optimizable<R>, Parameters, File) - Method in class Optimizers.ConjugateGradient
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- maximise(Optimizable<R>, Parameters) - Method in class Optimizers.GoldenSection
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- maximise(Optimizable<R>, Parameters, File) - Method in class Optimizers.GoldenSection
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- maximise(Optimizable<R>, Parameters) - Method in class Optimizers.NelderMead
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- maximise(Optimizable<R>, Parameters, File) - Method in class Optimizers.NelderMead
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- maximise(Optimizable<R>, Parameters) - Method in interface Optimizers.Optimizer
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Maximises the likelihood, logging to screen.
- maximise(Optimizable<R>, Parameters, File) - Method in interface Optimizers.Optimizer
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Maximises the likelihood, logging to a file.
- midPointRoot(String) - Method in class Trees.Tree
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Mid point roots the tree and returns a new tree
- Model - Class in Models
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Represents an evolutionary model.
- Model(RateCategory) - Constructor for class Models.Model
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Creates a new model with a single rate class
- Model(Map<RateCategory, String>) - Constructor for class Models.Model
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Creates a new model with multiple rate classes
- Model.ModelException - Exception in Models
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Exception thrown when there is a problem with the model
- Model.ModelException(String) - Constructor for exception Models.Model.ModelException
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Constructor when there is no underlying Throwable that caused the problem.
- Model.ModelException(String, Throwable) - Constructor for exception Models.Model.ModelException
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Constructor when there is an underlying Throwable that caused the problem.
- Models - package Models
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Provides classes for defining a phylogenetic model.
- ModelTest - package ModelTest
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- MRCA(List<String>) - Method in class Trees.Tree
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Returns the most recent common ancestor of a set of leaves.
- multiply(String, Real) - Method in class Likelihood.SiteLikelihood.NodeLikelihood
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This is a fudge to stop to allow this code to be reused in some
of the ancestor classes.
- multiply(String, double) - Method in class Likelihood.SiteLikelihood.NodeLikelihood
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This is a fudge to stop to allow this code to be reused in some
of the ancestor classes.
- multiply(Real) - Method in interface Maths.Real
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Multiplies this Real by another
- multiply(double) - Method in interface Maths.Real
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Multiplies this Real by a double
- multiply(Real) - Method in class Maths.SmallDouble
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- multiply(double) - Method in class Maths.SmallDouble
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- multiply(SquareMatrix) - Method in class Maths.SquareMatrix
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Multiplies this matrix by another (this × o) and returns a new
matrix as a result
- multiply(Real) - Method in class Maths.StandardDouble
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- multiply(double) - Method in class Maths.StandardDouble
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- multiplyBy(String) - Method in class Models.RateCategory
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Returns a new RateCategory where every position in the rate matrix is multiplied
by a given value
- multiplyip(Real) - Method in interface Maths.Real
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Multiplies this Real by another Real in place.
- multiplyip(double) - Method in interface Maths.Real
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Multiplies this Real by a double in place.
- multiplyip(Real) - Method in class Maths.SmallDouble
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- multiplyip(double) - Method in class Maths.SmallDouble
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- multiplyip(Real) - Method in class Maths.StandardDouble
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- multiplyip(double) - Method in class Maths.StandardDouble
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