Uses of Class
de.jstacs.models.phylo.PhyloTree

Packages that use PhyloTree

de.jstacs.models.hmm	The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.models.hmm.states.emissions.discrete
de.jstacs.models.phylo
de.jstacs.models.phylo.parser

Uses of PhyloTree in de.jstacs.models.hmm

Methods in de.jstacs.models.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.models.hmm.states.emissions.discrete

Constructors in de.jstacs.models.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.models.phylo

Methods in de.jstacs.models.phylo that return PhyloTree

PhyloTree

PhyloTree.clone()

Uses of PhyloTree in de.jstacs.models.phylo.parser

Methods in de.jstacs.models.phylo.parser that return PhyloTree

PhyloTree

NewickParser.tokenize() This method construct a PhyloTree from the given input stream