Package jebl.evolution.substmodel
Class WAG
java.lang.Object
jebl.evolution.substmodel.AbstractRateMatrix
jebl.evolution.substmodel.AminoAcidModel
jebl.evolution.substmodel.WAG
- All Implemented Interfaces:
Serializable
,Cloneable
,RateMatrix
WAG model of amino acid evolution (S. Whelan and N. Goldman 2000)
- Version:
- $Id: WAG.java 185 2006-01-23 23:03:18Z rambaut $
- Author:
- Korbinian Strimmer, Alexei Drummond
- See Also:
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic double[]
static void
getOriginalFrequencies
(double[] f) get the frequencies of the original data set that formed the basis for the estimation of the rate matrixMethods inherited from class jebl.evolution.substmodel.AbstractRateMatrix
getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getRelativeRates, getSequenceType, getTransitionProbabilities, getTransitionProbability, rebuild, scale, setDistance, setDistanceTranspose, setParametersNoScale
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Constructor Details
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WAG
public WAG(double[] f) constructor- Parameters:
f
- amino acid frequencies
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Method Details
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getOriginalFrequencies
public static void getOriginalFrequencies(double[] f) get the frequencies of the original data set that formed the basis for the estimation of the rate matrix- Parameters:
f
- array where amino acid frequencies will be stored
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getOriginalFrequencies
public static double[] getOriginalFrequencies()- Returns:
- the frequencies of the original data set that formed the basis for the estimation of the rate matrix
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getUniqueName
- Returns:
- a short unique human-readable identifier for this rate matrix.
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