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## calhoun.analysis.crf.features.supporting.phylogenetic
Class EvolutionaryModel

    java.lang.Object
      calhoun.analysis.crf.features.supporting.phylogenetic.EvolutionaryModel

All Implemented Interfaces:
  java.io.Serializable

    public class EvolutionaryModel

extends java.lang.Object
implements java.io.Serializable

See Also:
  Serialized Form

Constructor Summary
`EvolutionaryModel(PhylogeneticTreeFelsensteinOrder T, double[] pi, NucleotideSubstitutionModel R)`

Method Summary
`double` | `logprob(MultipleAlignmentInputSequence.MultipleAlignmentColumn col, boolean conditionref)`
`double` | `logprobRC(MultipleAlignmentInputSequence.MultipleAlignmentColumn col, boolean conditionref)`
`void` | `summarize()`

Methods inherited from class java.lang.Object
`equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Constructor Detail

### EvolutionaryModel

    public EvolutionaryModel(PhylogeneticTreeFelsensteinOrder T,
                             double[] pi,
                             NucleotideSubstitutionModel R)

Method Detail

### logprobRC

    public double logprobRC(MultipleAlignmentInputSequence.MultipleAlignmentColumn col,
                            boolean conditionref)

### logprob

    public double logprob(MultipleAlignmentInputSequence.MultipleAlignmentColumn col,
                          boolean conditionref)

### summarize

    public void summarize()

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