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F

FastaAlignment - Class in Alignments
Static classes for reading/writing sequence alignment in FASTA format
Felsenstein81(Parameters) - Static method in class Models.DNAModelFactory
Creates an instance of a Felsenstein 81 model
Felsenstein81() - Static method in class Models.DNAModelFactory
Creates an instance of a Felsenstein 81 model
Felsenstein81_Gamma(Parameters, int) - Static method in class Models.DNAModelFactory
Creates an instance of a JFelsenstein 81 model with gamma-distributed rate across sites
Felsenstein81_Gamma(int) - Static method in class Models.DNAModelFactory
Creates an instance of a JFelsenstein 81 model with gamma-distributed rate across sites
FitzJohnRoot - Class in Likelihood
Root class for the FitzJohn et al 2009 method
FitzJohnRoot(Set<String>) - Constructor for class Likelihood.FitzJohnRoot
Default constructor
fromFile(File) - Static method in class Alignments.Ambiguous
Reads in ambiguous data information from a file.
fromFile(File) - Static method in class Alignments.DuplicationAlignment
Creates a duplication alignment from a file.
fromFile(File, Ambiguous) - Static method in class Alignments.DuplicationAlignment
Creates a duplication alignment which contains ambiguous data.
fromFile(File) - Static method in class Alignments.FastaAlignment
Creates a sequence alignment from a file.
fromFile(File, Ambiguous) - Static method in class Alignments.FastaAlignment
Creates a sequence alignment from a file with ambiguous data.
fromFile(File) - Static method in class Alignments.GenericAlignment
Creates a sequence alignment from a file.
fromFile(File, Ambiguous) - Static method in class Alignments.GenericAlignment
Creates a sequence alignment from a file with ambiguous data.
fromFile(File) - Static method in class Alignments.PhylipAlignment
Creates a sequence alignment from a file.
fromFile(File, Ambiguous) - Static method in class Alignments.PhylipAlignment
Creates a sequence alignment from a file with ambiguous data.
fromFile(File) - Static method in class Models.Model
Creates a new model from a file.
fromFile(File) - Static method in class Models.RateCategory
Creates an instance from the information in a file.
fromFile(File) - Static method in class Parameters.Parameters
Reads parameters from a file.
fromFile(File) - Static method in class Trees.Tree
Creates a tree from a file containing a Newick string
fromFile(File) - Static method in class Utils.SetSettings
Reads settings from a file and returns an instance of this class.
fromFileAndCommandLine(File, String[]) - Static method in class Utils.SetSettings
Returns settings from a file and the command line and returns an instance of this class.
fromNewickString(String) - Static method in class Trees.Tree
Creates a tree from a newick string
FunctionParser - Interface in Maths
Interface for a function parser.
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