Package | Description |
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Likelihood |
Provides classes for calculating the likelihood of a tree given a model and
an alignment.
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Models |
Provides classes for defing a phylogenetic model.
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Modifier and Type | Method and Description |
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RateCategory |
Likelihood.SiteLikelihood.getMostProbableRateCategory()
Gets the most probable rate category
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Modifier and Type | Method and Description |
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java.util.Set<RateCategory> |
Probabilities.getRateCategory()
Gets the set of RateClasses that we have calculated probailities for
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Modifier and Type | Method and Description |
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double |
Probabilities.getFreq(RateCategory r,
java.lang.String state)
Gets the root frequency for a specified state under a specified RateClass
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double |
Probabilities.getP(RateCategory r,
Branch b,
java.lang.String startState,
java.lang.String endState)
Gets a specific probability for a change from one state to another along
a specific branch under a specific RateClass
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double |
Likelihood.SiteLikelihood.getRateCategoryProbability(RateCategory rc)
Gets the probability of being in a rate category
|
Likelihood.RateLikelihood |
Likelihood.SiteLikelihood.getRateLikelihood(RateCategory rate)
Get the likelihood for a single rate class
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double |
Probabilities.getRateP(RateCategory r)
Gets the probability of a rate class
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Modifier and Type | Method and Description |
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static RateCategory |
RateCategory.fromFile(java.io.File mfile)
Creates an instance from the information in a file.
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Modifier and Type | Method and Description |
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java.util.Set<RateCategory> |
Model.getRates()
Gets a set of rate classes in the model
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java.util.Iterator<RateCategory> |
Model.iterator() |
Modifier and Type | Method and Description |
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static Model |
Model.gammaRates(RateCategory r,
java.lang.String gamma,
int cats)
Creates a new model with multiple rate classes distributed by a gamma
distribution (see Yang 1993) based on a single rate class
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double |
Model.getFreq(RateCategory r)
Gets the frquency of a rate class
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Constructor and Description |
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Model(RateCategory r)
Creates a new model with a single rate class
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Constructor and Description |
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Model(java.util.Map<RateCategory,java.lang.String> freq)
Creates a new model with multiple rate classes
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