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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
Reads in amiguous data information from a file.
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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