- 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.