Package | Description |
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pal.substmodel |
Classes describing substitution models, i.e.
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Modifier and Type | Method and Description |
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static GeneralREVRateMatrix |
GeneralREVRateMatrix.createGTR()
Create a rate matrix equivalent to the GTR model
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static GeneralREVRateMatrix |
GeneralREVRateMatrix.createGTR(double[] defaultParameters)
Create a rate matrix equivalent to the GTR model
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static GeneralREVRateMatrix |
GeneralREVRateMatrix.createGTR(double a,
double b,
double c,
double d,
double e)
Create a rate matrix equivalent to the GTR model
Parameters laid out
*
-> + A C G T
A * a b c
C * * d e
G * * * 1
T * * * *
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static GeneralREVRateMatrix |
GeneralREVRateMatrix.createHKY()
Create a rate matrix equivalent to the HKY model, the one parameter will be kappa
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static GeneralREVRateMatrix |
GeneralREVRateMatrix.createHKY(double defaultKappa)
Create a rate matrix equivalent to the HKY model, the one parameter will be kappa
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