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M

main(String[]) - Static method in class Executable.Example
Main function
main(String[]) - Static method in class Executable.GeLL
Main function
MapUtils - Class in Utils
Utility class for maps
Maths - package Maths
Provides maths classes.
MathsParse - Class in Maths
Class used to parse an equation represented by a string and return the result.
MathsParse(FunctionParser...) - Constructor for class Maths.MathsParse
Default constructor.
matrix() - Method in class Parameters.Parameter
Whether this parameter is in a rate matrix.
maximise(Calculator, Parameters) - Method in class Optimizers.GoldenSection
 
maximise(Calculator, Parameters, File) - Method in class Optimizers.GoldenSection
 
maximise(Calculator, Parameters) - Method in class Optimizers.NelderMead
 
maximise(Calculator, Parameters, File) - Method in class Optimizers.NelderMead
 
maximise(Calculator, Parameters) - Method in interface Optimizers.Optimizer
Maximises the likelihood, logging to screen.
maximise(Calculator, Parameters, File) - Method in interface Optimizers.Optimizer
Maximises the likelihood, logging to a file.
meetsConstrains(Site) - Method in class Constraints.SiteConstraints
Tests whether a given site (that should include data for internal nodes) meets the defined constraints
midPointRoot(String) - Method in class Trees.Tree
Mid point roots the tree and returns a new tree
Model - Class in Models
Represents an evolutionary model.
Model(RateCategory) - Constructor for class Models.Model
Creates a new model with a single rate class
Model(Map<RateCategory, String>) - Constructor for class Models.Model
Creates a new model with multiple rate classes
Model.ModelException - Exception in Models
Exception thrown when there is a problem with the model
Model.ModelException(String) - Constructor for exception Models.Model.ModelException
Constructor when there is no underlying Throwable that caused the problem.
Model.ModelException(String, Throwable) - Constructor for exception Models.Model.ModelException
Constructor when there is an underlying Throwable that caused the problem.
Models - package Models
Provides classes for defing a phylogenetic model.
MRCA(List<String>) - Method in class Trees.Tree
Returns the most recent common ancestor of a set of leaves
multiply(SquareMatrix) - Method in class Maths.SquareMatrix
Multiplies this matrix by another (this × o) and returns a new matrix as a result
multiply(K, double) - Method in class Utils.ToDoubleHashMap
Multiply the value associated with a key
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