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## Uses of Class
de.jstacs.sequenceScores.statisticalModels.trainable.phylo.PhyloTree

Packages that use PhyloTree
de.jstacs.sequenceScores.statisticalModels.trainable.hmm | The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete |
de.jstacs.sequenceScores.statisticalModels.trainable.phylo |
de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser |

Uses of PhyloTree in de.jstacs.sequenceScores.statisticalModels.trainable.hmm

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm with parameters of type PhyloTree
`static AbstractHMM` | `HMMFactory.createSunflowerHMM(HMMTrainingParameterSet pars, AlphabetContainer con, double ess, int expectedSequenceLength, boolean startCentral, PhyloTree[] t, double[] motifProb, int[] motifLength)` This method creates a first order sunflower HMM allowing phylogenetic emissions.

Uses of PhyloTree in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete with parameters of type PhyloTree
`PhyloDiscreteEmission(AlphabetContainer con, double[] hyperParams, PhyloTree t)` This is a simple constructor for a `DiscreteEmission` defining the individual hyper parameters.
`PhyloDiscreteEmission(AlphabetContainer con, double ess, PhyloTree t)` This is a simple constructor for a `PhyloDiscreteEmission` based on the equivalent sample size.

Uses of PhyloTree in de.jstacs.sequenceScores.statisticalModels.trainable.phylo

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.phylo that return PhyloTree
`PhyloTree` | `PhyloTree.clone()`

Uses of PhyloTree in de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser that return PhyloTree
`PhyloTree` | `NewickParser.tokenize()` This method construct a `PhyloTree` from the given input stream

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