- Felsenstein81(Parameters) - 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
- fromFile(File) - Static method in class Alignments.Ambiguous
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Reads in amiguous data information from a file.
- fromFile(File) - Static method in class Models.Model
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Creates a new model from a file.
- fromFile(File) - Static method in class Models.RateCategory
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Creates an instance from the information in a file.
- fromFile(File) - Static method in class Parameters.Parameters
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Reads parameters from a file.
- fromFile(File) - Static method in class Trees.Tree
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Creates a tree from a file containing a Newick string
- fromFile(File) - Static method in class Utils.SetSettings
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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
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Creates a tree from a newick string
- FunctionParser - Interface in Maths
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Interface for a function parser.