Method Detail

• isCICompatible

  boolean isCICompatible()

  Returns:

  true if it possible to do Confidence Interval stuff

• inferCI

  SUPGMABase.CISummary inferCI​(AlgorithmCallback callback,
                               int numberOfReplicates,
                               SimulatedAlignment.Factory alignmentFactory,
                               SubstitutionModel evolutionaryModel,
                               LMSSolver solver)

• generateSUPGMATree

  Tree generateSUPGMATree​(ClusterTree.ClusteringMethod cm)

• generateSUPGMATree

  Tree generateSUPGMATree​(AlgorithmCallback callback,
                          ClusterTree.ClusteringMethod cm,
                          DistanceMatrixGenerator replicateSource,
                          int numberOfAlignmentBootstrapReplicates,
                          LMSSolver solver)

• simulateTrees

  Tree[] simulateTrees​(int numberOfTreesToSimulate,
                       AlgorithmCallback callback,
                       LMSSolver solver)

• simulateTree

  Tree simulateTree()

• generateHTML

  java.lang.String generateHTML()