Uses of Interface
pal.tree.Tree

Packages that use Tree
pal.coalescent Classes to model population genetic processes using the coalescent. 
pal.distance Classes for reading and generating distance matrices, including computation of pairwise distances for sequence data (maximum-likelihood and observed distances). 
pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters. 
pal.gui GUI components for some special objects (e.g., trees). 
pal.mep Classes for the analysis of "measurably evolving populations" (mep). 
pal.statistics Classes with useful for statistics (normal distribution, Gamma distribution, chi-square distribution, exponential distribution, likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.) 
pal.supgma   
pal.tree Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint). 
pal.treesearch   
pal.xml Utility classes for converting PAL objects to and from XML documents. 
 

Uses of Tree in pal.coalescent
 

Classes in pal.coalescent that implement Tree
 class DemographicClockTree
          Provides parameter interface to a clock-like genealogy which is assumed to have some demographic pattern of theta (diversity) as well as branch parameters (the minimal node height differences at each internal node).
 

Methods in pal.coalescent that return Tree
 Tree SerialCoalescentGenerator.generateTree()
           
 Tree[] SerialCoalescentGenerator.generateTrees(AlgorithmCallback callback)
          If callback request stop then returns trees creating thus far
 Tree SerialCoalescentSimulator.getTree()
           
 Tree[] SerialCoalescentGenerator.Results.getTrees()
           
 

Methods in pal.coalescent with parameters of type Tree
static CoalescentIntervals IntervalsExtractor.extractFromClockTree(Tree tree)
          extracts intervals from clock tree.
static CoalescentIntervals IntervalsExtractor.extractFromClockTree(Tree tree, double minSize)
          extracts intervals from clock tree.
static CoalescentIntervals IntervalsExtractor.extractFromTree(Tree tree)
          extracts intervals from serial clock tree.
static CoalescentIntervals IntervalsExtractor.extractFromTree(Tree tree, MutationRateModel muModel)
          extracts intervals in generation times from serial clock tree (in mutation times) after taking into account mutation rate model.
 

Constructors in pal.coalescent with parameters of type Tree
DemographicClockTree(Tree t, DemographicModel model)
          take any tree and afford it with an interface suitable for a clock-like genealogy, under a certain demographic assumption.
SerialCoalescentGenerator.Results(Tree[] trees)
           
SerialCoalescentGenerator.Results(Tree[] trees, Alignment[] alignments)
           
SkylinePlot(Tree tree, double epsilon)
          Construct skyline plot from tree
 

Uses of Tree in pal.distance
 

Methods in pal.distance with parameters of type Tree
static DistanceMatrixGenerator DistanceMatrixGenerator.Utils.createParametric(Tree baseTree, SubstitutionModel sm, int numberOfSites)
          Silly idea stuff
 

Uses of Tree in pal.eval
 

Methods in pal.eval that return Tree
 Tree ChiSquareValue.getTree()
          Returns the (parameterized) tree of this likelihood value.
 Tree SimpleLikelihoodCalculator.getTree()
           
 Tree LikelihoodValue.getTree()
          Returns the (potentially parameterized) tree of this likelihood value.
static Tree LikelihoodTool.optimiseClockConstrained(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel)
          Optimise the branches of a tree with regard to maximum likelihood, with a molecular clock assumption, that is, constrained such that all tips are contemporaneous, the tree is treated as rooted.
static Tree LikelihoodTool.optimiseMRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateStore)
          Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu - one for each sampling interval.
static Tree LikelihoodTool.optimiseMRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateChangeTimes, double[] rateStore)
          Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu, over general time intervals.
static Tree LikelihoodTool.optimiseSRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateStore)
          Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and a single mutation rate parameter.
static Tree LikelihoodTool.optimiseUnrooted(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel)
          Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).
 

Methods in pal.eval with parameters of type Tree
static double LikelihoodTool.calculateLogLikelihood(Tree tree, Alignment alignment, SubstitutionModel model)
          Calculate the log likelihood of a particular set of phylogenetic data
static Tree LikelihoodTool.optimiseClockConstrained(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel)
          Optimise the branches of a tree with regard to maximum likelihood, with a molecular clock assumption, that is, constrained such that all tips are contemporaneous, the tree is treated as rooted.
static double LikelihoodOptimiser.optimiseModel(Tree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
          Optimise model parameters only to acheive maximum likelihood using a combined stategy.
static Tree LikelihoodTool.optimiseMRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateStore)
          Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu - one for each sampling interval.
static Tree LikelihoodTool.optimiseMRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateChangeTimes, double[] rateStore)
          Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu, over general time intervals.
static Tree LikelihoodTool.optimiseSRDT(Tree tree, Alignment alignment, SubstitutionModel model, TimeOrderCharacterData tocd, boolean optimiseModel, double[] rateStore)
          Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and a single mutation rate parameter.
static Tree LikelihoodTool.optimiseUnrooted(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel)
          Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).
 void ChiSquareValue.setTree(Tree t)
          define (parameterized) tree
 void FastLikelihoodCalculator.setTree(Tree t)
           
 void SimpleLikelihoodCalculator.setTree(Tree t)
          define tree ,(must only be called only after a site pattern has been defined).
 void LikelihoodValue.setTree(Tree t)
          define (parameterized) tree ,(must only be called only after a site pattern has been defined).
 void GeneralLikelihoodCalculator.setup(Tree t, SubstitutionModel model)
           
 

Constructors in pal.eval with parameters of type Tree
FastLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model)
          Constructor taking site pattern, tree and model.
GeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, RateMatrix model)
          Constructor taking site pattern, tree and a rate matrix.
GeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, RateMatrix model, RateDistribution distribution)
          Constructor taking site pattern, tree rate matrix, and a rate distribution
GeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, SubstitutionModel model)
          Constructor taking site pattern, tree and a general substitution model.
LikelihoodOptimiser(Tree tree, Alignment alignment, SubstitutionModel model)
           
SimpleLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model)
           
 

Uses of Tree in pal.gui
 

Methods in pal.gui that return Tree
protected  Tree TreePainter.getTree()
           
 

Methods in pal.gui with parameters of type Tree
 void TreePainter.setTree(Tree tree)
           
 void TreeComponent.setTree(Tree tree)
           
 void TreePainter.setTreeImpl(Tree tree)
          may be implemented by sub classes
 void TreePainterCircular.setTreeImpl(Tree t)
           
 

Constructors in pal.gui with parameters of type Tree
TreeComponent(Tree tree)
           
TreeComponent(Tree tree, boolean usingSymbols)
           
TreeComponent(Tree tree, java.lang.String title)
           
TreeComponent(Tree tree, java.lang.String title, boolean showTitle)
           
TreeComponent(Tree tree, TimeOrderCharacterData tocd, boolean usingSymbols)
           
TreePainter(Tree toDisplay, java.lang.String title, boolean showTitle)
           
TreePainterCircular(Tree toDisplay, java.lang.String title, boolean showTitle)
           
TreePainterNormal(Tree toDisplay, java.lang.String title, boolean showTitle)
           
 

Uses of Tree in pal.mep
 

Methods in pal.mep that return Tree
 Tree DeltaModel.Instance.generateAlternativeRepresentation(Tree expectedSubstitutionsTree)
           
 

Methods in pal.mep with parameters of type Tree
 Tree DeltaModel.Instance.generateAlternativeRepresentation(Tree expectedSubstitutionsTree)
           
 

Uses of Tree in pal.statistics
 

Methods in pal.statistics that return Tree
 Tree LikelihoodEvaluator.MLResult.getOptimisedTree()
           
 Tree LikelihoodEvaluator.SimpleMLResult.getOptimisedTree()
           
 Tree[] GeneralTopologyPool.getOriginalOptimisedTrees()
           
 

Methods in pal.statistics with parameters of type Tree
 double LikelihoodEvaluator.calculateLikelihood(Tree tree, Alignment alignment)
           
 LikelihoodEvaluator.MLResult LikelihoodEvaluator.getMLOptimised(Tree tree, Alignment alignment, AlgorithmCallback callback)
           
 double ReplicateLikelihoodEvaluator.getReplicateLogLikelihood(Tree tree, Alignment alignment)
           
 

Constructors in pal.statistics with parameters of type Tree
GeneralTopologyPool(Tree[] topologies, LikelihoodEvaluator baseCalculator, ReplicateLikelihoodEvaluator replicateCalculator, Alignment baseAlignment, AlignmentGenerator replicateGenerator)
           
LikelihoodEvaluator.SimpleMLResult(double logLikelihood, Tree optimisedTree)
           
 

Uses of Tree in pal.supgma
 

Classes in pal.supgma that implement Tree
 class SUPGMATree
          constructs an SUPGMA tree from pairwise distances.
 

Methods in pal.supgma that return Tree
 Tree SUPGMABase.generateAlignmentBootstrappedSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, SUPGMABase.PopulationParameters pp, int numberOfReplicates, LMSSolver solver)
           
 Tree SUPGMABase.PopulationParameters.generateSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, DistanceMatrixGenerator replicateSource, int numberOfAlignmentBootstrapReplicates, LMSSolver solver)
           
 Tree SUPGMABase.PopulationParameters.generateSUPGMATree(ClusterTree.ClusteringMethod cm)
           
 Tree SUPGMABase.PopulationParameters.simulateTree()
           
 Tree[] SUPGMABase.PopulationParameters.simulateTrees(int numberOfTreesToSimulate, AlgorithmCallback callback, LMSSolver solver)
           
 Tree SUPGMABase.solve(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, LMSSolver solver)
           
 

Uses of Tree in pal.tree
 

Subinterfaces of Tree in pal.tree
 interface ParameterizedTree
          abstract base class for a tree with an Parameterized interface
 

Classes in pal.tree that implement Tree
 class ClockTree
          provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)
 class ClusterTree
           
 class LogParameterizedTree
          This class logarithmically transforms tree parameters.
 class MutationRateModelTree
          Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).
 class NeighborJoiningTree
          constructs a neighbor-joining tree from pairwise distances

Saitou, N., and Nei, M., (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees.
static class ParameterizedTree.ParameterizedTreeBase
          For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)
 class ReadTree
          constructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted trees
 class SimpleTree
          data structure for a binary/non-binary rooted/unrooted trees
static class Tree.TreeBase
           
 class UnconstrainedTree
          provides parameter interface to an unconstrained tree (parameters are all available branch lengths)
 class UPGMATree
          Deprecated. Use ClusterTree
 

Methods in pal.tree that return Tree
static Tree TreeTool.createNeighbourJoiningTree(DistanceMatrix dm)
          Neighbour-joining tree construction based on a distance matrix
static Tree TreeTool.createNeighbourJoiningTree(double[][] dm, java.lang.String[] otuNames)
          Neighbour-joining tree construction based on a distance matrix
static Tree TreeTool.createUPGMA(DistanceMatrix dm)
          UPGMA tree construction based on a distance matrix
static Tree TreeTool.createUPGMATree(double[][] dm, java.lang.String[] otuNames)
          UPGMA tree construction based on a distance matrix
 Tree TreeRestricter.generateTree()
           
static Tree TreeUtils.generationsToMutations(Tree generationTree, MutationRateModel muModel)
          Takes a tree (in generation units) and returns a scaled version of it (in mutation units).
static Tree TreeUtils.generationsToMutations(Tree generationTree, MutationRateModel muModel, double generationTime)
          Takes a tree (in generation units) and returns a scaled version of it (in mutation units).
static Tree[] TreeManipulator.getAllRootingsBy(Tree base, java.lang.String[] outgroupNames)
          Roots a tree by an outgroup
 Tree[] TreeManipulator.getAllTreesRootedBy(java.lang.String[] outgroupNames)
           
 Tree TreeManipulator.getAsInputRootingTree()
          A method for recovering the input (construction) tree (with the EXPANSION/MIMIC/REDUCED differences)
protected  Tree ParameterizedTree.ParameterizedTreeBase.getBaseTree()
           
static Tree TreeUtils.getBootstrapSupportByCladeTree(java.lang.String attributeName, Tree baseTree, Tree[] alternativeTrees)
          Deprecated. Use getReplicateCladeSupport instead
 Tree UnconstrainedTree.getCopy()
           
 Tree ParameterizedTree.ParameterizedTreeBase.getCopy()
          The cheapy copy that just creates a SimpleTree
 Tree ClockTree.getCopy()
           
 Tree Tree.getCopy()
           
 Tree SimpleTree.getCopy()
           
 Tree MutationRateModelTree.getCopy()
           
 Tree TreeManipulator.getDefaultRootTree()
           
 Tree[] TreeManipulator.getEveryRoot()
           
static Tree[] TreeManipulator.getEveryRoot(Tree base)
          Obtains every rooting of a base tree
static Tree TreeManipulator.getMidpointRooted(Tree base)
          Returns the mid point rooting of a tree.
static Tree TreeTool.getMidPointRooted(Tree t)
          Root a tree around it's midpoint.
 Tree TreeManipulator.getMidPointRootedTree()
           
 Tree TreeGenerator.getNextTree(AlgorithmCallback callback)
           
static Tree TreeUtils.getNumberRelabelledTree(Tree baseTree, IdGroup ids)
          Create a new tree such that the labels are redifined from a base tree in such a manner: For each leaf label If the base label is not a number the new label is just the original label If the base label is a number the new label appropriately index label from a set identifiers
static Tree TreeUtils.getReplicateCladeSupport(java.lang.String attributeName, Tree baseTree, TreeGenerator treeGenerator, int numberOfReplicates, AlgorithmCallback callback)
          Generates a tree which is identical to baseTree but has attributes (defined by attributeName) at all internal nodes excluding the root node signifying (as a value between 0 and 100) the replicate support by clade (that is the proportion of replicates that produce the sub clade under that node)
static Tree TreeTool.getRooted(Tree t, java.lang.String[] outgroupMembers)
          Root a tree by an outgroup.
static Tree TreeManipulator.getRootedBy(Tree base, java.lang.String[] outgroupNames)
          Roots a tree by an outgroup
static Tree TreeManipulator.getRootedBy(Tree base, java.lang.String[] outgroupNames, double ingroupBranchLength)
          Roots a tree by an outgroup
static Tree TreeUtils.getScaled(Tree oldTree, double rate)
          Takes a tree and returns a scaled version of it.
static Tree TreeUtils.getScaled(Tree oldTree, double rate, int newUnits)
          Takes a tree and returns a scaled version of it.
static Tree TreeUtils.getScaled(Tree mutationRateTree, MutationRateModel muModel)
          Takes a tree and returns a scaled version of it.
static Tree TreeUtils.getScaled(Tree mutationRateTree, MutationRateModel muModel, int newUnits)
          Takes a tree and returns a scaled version of it.
 Tree TreeManipulator.getTreeRootedAbove(Node n)
           
 Tree TreeManipulator.getTreeRootedBy(java.lang.String[] outgroupNames)
           
 Tree TreeManipulator.getTreeRootedBy(java.lang.String[] outgroupNames, double ingroupBranchLength)
           
static Tree TreeTool.getUnrooted(Tree t)
          Unroot a tree (makes the base of the tree a trification).
static Tree TreeManipulator.getUnrooted(Tree base)
          Unroots a tree
 Tree TreeManipulator.getUnrootedTree()
          return unrooted node
static Tree Local.local(Tree tree)
           
static Tree Local.local(Tree tree, double scaleFactor)
          This method does a local interchange on the given tree: Note the original tree is modified.
static Tree TreeUtils.mutationsToGenerations(Tree mutationTree, MutationRateModel muModel)
          Takes a tree (in mutation units) and returns a scaled version of it (in generation units).
 Tree TreeOperation.operateOn(Tree tree)
          Operates on input tree.
static Tree TreeTool.readTree(java.io.Reader r)
          Read a tree from an input source.
static Tree TreeUtils.scale(Tree oldTree, double rate, int newUnits)
          Deprecated. use getScaled()
static Tree TreeUtils.scale(Tree mutationRateTree, MutationRateModel muModel)
          Deprecated. use getScaled()
static Tree TreeUtils.scale(Tree mutationRateTree, MutationRateModel muModel, int newUnits)
          Deprecated. use getScaled()
static Tree Local.stochasticNNI(Tree tree)
           
 

Methods in pal.tree with parameters of type Tree
static void CladeSystem.calculateCladeProbabilities(Tree tree, CladeSystem[] cladeSystems)
           
static void RootedTreeUtils.collectProportions(Tree tree, java.util.Vector trees)
           
static void TreeUtils.computeAllDistances(Tree tree, int a, double[] dist, double[] idist, boolean countEdges, double epsilon)
           
static double TreeUtils.computeDistance(Tree tree, int a, int b)
          compute distance between two external nodes
static Alignment TreeUtils.extractAlignment(Tree tree)
          Extracts an alignment from a tree.
static Alignment TreeUtils.extractAlignment(Tree tree, boolean leaveSeqsInTree)
          Extracts an alignment from a tree.
static TimeOrderCharacterData TreeUtils.extractTimeOrderCharacterData(Tree tree, int units)
          Extracts a time order character data from a tree.
 SimulatedAlignment SimulatedAlignment.Factory.generateAlignment(Tree tree)
          Generate a simulated alignment based on input tree
 SimulatedAlignment[] SimulatedAlignment.Factory.generateAlignments(Tree[] trees, AlgorithmCallback callback)
          Generate an array of simulated alignments based on an array of input trees
 ParameterizedTree ParameterizedTree.Factory.generateNewTree(Tree base)
          Generate a new parameterized tree wrapped around base
static Tree TreeUtils.generationsToMutations(Tree generationTree, MutationRateModel muModel)
          Takes a tree (in generation units) and returns a scaled version of it (in mutation units).
static Tree TreeUtils.generationsToMutations(Tree generationTree, MutationRateModel muModel, double generationTime)
          Takes a tree (in generation units) and returns a scaled version of it (in mutation units).
static Tree[] TreeManipulator.getAllRootingsBy(Tree base, java.lang.String[] outgroupNames)
          Roots a tree by an outgroup
static Tree TreeUtils.getBootstrapSupportByCladeTree(java.lang.String attributeName, Tree baseTree, Tree[] alternativeTrees)
          Deprecated. Use getReplicateCladeSupport instead
static Tree TreeUtils.getBootstrapSupportByCladeTree(java.lang.String attributeName, Tree baseTree, Tree[] alternativeTrees)
          Deprecated. Use getReplicateCladeSupport instead
static CladeSystem CladeSystem.getClades(IdGroup idGroup, Tree tree)
          creates a clade system from a tree (using a pre-specified order of sequences)
static CladeSystem CladeSystem.getClades(Tree tree)
          creates a clade system from a tree (using tree-induced order of sequences)
static CladeSystem[] CladeSystem.getCladeSystems(Tree[] trees)
           
static Tree[] TreeManipulator.getEveryRoot(Tree base)
          Obtains every rooting of a base tree
static TreeIterator TreeManipulator.getEveryRootIterator(Tree base)
          Obtains every rooting of a base tree
static IdGroup TreeUtils.getLeafIdGroup(Tree tree)
          get list of the identifiers of the external nodes
static Tree TreeManipulator.getMidpointRooted(Tree base)
          Returns the mid point rooting of a tree.
static Tree TreeTool.getMidPointRooted(Tree t)
          Root a tree around it's midpoint.
static Node TreeUtils.getNodeByName(Tree tree, java.lang.String name)
           
static Tree TreeUtils.getNumberRelabelledTree(Tree baseTree, IdGroup ids)
          Create a new tree such that the labels are redifined from a base tree in such a manner: For each leaf label If the base label is not a number the new label is just the original label If the base label is a number the new label appropriately index label from a set identifiers
static Node TreeUtils.getRandomNode(Tree tree)
          Returns a uniformly distributed random node from the tree, including both internal and external nodes.
static Tree TreeUtils.getReplicateCladeSupport(java.lang.String attributeName, Tree baseTree, TreeGenerator treeGenerator, int numberOfReplicates, AlgorithmCallback callback)
          Generates a tree which is identical to baseTree but has attributes (defined by attributeName) at all internal nodes excluding the root node signifying (as a value between 0 and 100) the replicate support by clade (that is the proportion of replicates that produce the sub clade under that node)
static double TreeUtils.getRobinsonFouldsDistance(SplitSystem s1, Tree t2)
          computes Robinson-Foulds (1981) distance between two trees
static double TreeUtils.getRobinsonFouldsDistance(Tree t1, Tree t2)
          computes Robinson-Foulds (1981) distance between two trees
static double TreeUtils.getRobinsonFouldsRescaledDistance(SplitSystem s1, Tree t2)
          computes Robinson-Foulds (1981) distance between two trees rescaled to a number between 0 and 1
static double TreeUtils.getRobinsonFouldsRescaledDistance(Tree t1, Tree t2)
          computes Robinson-Foulds (1981) distance between two trees rescaled to a number between 0 and 1
static Tree TreeTool.getRooted(Tree t, java.lang.String[] outgroupMembers)
          Root a tree by an outgroup.
static Tree TreeManipulator.getRootedBy(Tree base, java.lang.String[] outgroupNames)
          Roots a tree by an outgroup
static Tree TreeManipulator.getRootedBy(Tree base, java.lang.String[] outgroupNames, double ingroupBranchLength)
          Roots a tree by an outgroup
static Tree TreeUtils.getScaled(Tree oldTree, double rate)
          Takes a tree and returns a scaled version of it.
static Tree TreeUtils.getScaled(Tree oldTree, double rate, int newUnits)
          Takes a tree and returns a scaled version of it.
static Tree TreeUtils.getScaled(Tree mutationRateTree, MutationRateModel muModel)
          Takes a tree and returns a scaled version of it.
static Tree TreeUtils.getScaled(Tree mutationRateTree, MutationRateModel muModel, int newUnits)
          Takes a tree and returns a scaled version of it.
static SplitSystem SplitUtils.getSplits(IdGroup idGroup, Tree tree)
          creates a split system from a tree (using a pre-specified order of sequences)
static SplitSystem SplitUtils.getSplits(Tree tree)
          creates a split system from a tree (using tree-induced order of sequences)
static Tree TreeTool.getUnrooted(Tree t)
          Unroot a tree (makes the base of the tree a trification).
static Tree TreeManipulator.getUnrooted(Tree base)
          Unroots a tree
static void TreeUtils.labelInternalNodes(Tree tree)
          Labels the internal nodes of the tree using numbers starting from 0.
static Tree Local.local(Tree tree)
           
static Tree Local.local(Tree tree, double scaleFactor)
          This method does a local interchange on the given tree: Note the original tree is modified.
static int[] TreeUtils.mapExternalIdentifiers(IdGroup idGroup, Tree tree)
          map external identifiers in the tree to a set of given identifiers (which can be larger than the set of external identifiers but must contain all of them) NOTE: for efficiency it is assumed that the node lists of the tree are correctly maintained.
static Tree TreeUtils.mutationsToGenerations(Tree mutationTree, MutationRateModel muModel)
          Takes a tree (in mutation units) and returns a scaled version of it (in generation units).
 Tree TreeOperation.operateOn(Tree tree)
          Operates on input tree.
static void Local.print4TaxonTree(Tree tree, java.io.PrintWriter out)
           
static void TreeUtils.printNH(Tree tree, java.io.PrintWriter out)
          print a this tree in New Hampshire format (including distances and internal labels)
static void TreeUtils.printNH(Tree tree, java.io.PrintWriter out, boolean printLengths, boolean printInternalLabels)
          print this tree in New Hampshire format
 void TreeDistanceMatrix.recompute(Tree t)
           
static void TreeUtils.renameNodes(Tree tree, java.util.Hashtable table)
          Given a translation table where the keys are the current identifier names and the values are the new identifier names, this method replaces the current identifiers in the tree with new identifiers.
static void TreeUtils.report(Tree tree, java.io.PrintWriter out)
           
static void TreeUtils.reroot(Tree tree, Node node)
           
static void TreeUtils.rotateByLeafCount(Tree tree)
          Rotates branches by leaf count.
static Tree TreeUtils.scale(Tree oldTree, double rate, int newUnits)
          Deprecated. use getScaled()
static Tree TreeUtils.scale(Tree mutationRateTree, MutationRateModel muModel)
          Deprecated. use getScaled()
static Tree TreeUtils.scale(Tree mutationRateTree, MutationRateModel muModel, int newUnits)
          Deprecated. use getScaled()
protected  void ParameterizedTree.ParameterizedTreeBase.setBaseTree(Tree baseTree)
           
static Tree Local.stochasticNNI(Tree tree)
           
 

Constructors in pal.tree with parameters of type Tree
ClockTree(Tree t)
          take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).
MutationRateModelTree(Tree t, TimeOrderCharacterData tocd, MutationRateModel model)
          take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).
MutationRateModelTree(Tree t, TimeOrderCharacterData tocd, MutationRateModel model, boolean includeModelParameters)
          take any tree and afford it with an interface suitable for a clock-like tree (parameters are the minimal node height differences at each internal node).
ParameterizedTree.ParameterizedTreeBase(Tree baseTree)
           
SimpleTree(Tree tree)
          clone constructor
SimpleTree(Tree tree, boolean keepIdentifiers)
          clone constructor
SimpleTree(Tree tree, LabelMapping lm)
          clone constructor
SimulatedAlignment(int sites, Tree t, SubstitutionModel m)
          Inititalisation
TreeDistanceMatrix(Tree t)
          compute induced distance matrix using actual branch lengths (using tree-induced order of sequences)
TreeDistanceMatrix(Tree t, boolean countEdges, double epsilon)
          compute induced distance matrix (using tree-induced order of sequences)
TreeDistanceMatrix(Tree t, IdGroup idGroup)
          compute induced distance matrix using actual branch lengths
TreeDistanceMatrix(Tree t, IdGroup idGroup, boolean countEdges, double epsilon)
          compute induced distance matrix
TreeManipulator(Tree base)
          Construct a TreeManipulator based around a normal tree
TreeManipulator(Tree base, int constructionMode)
          Construct a TreeManipulator based around a normal tree
TreeRestricter(Tree t, java.lang.String[] names, boolean inclusion)
           
UnconstrainedTree(Tree t)
          take any tree and afford it with an interface suitable for an unconstrained tree (parameters are all available branch lengths)
 

Uses of Tree in pal.treesearch
 

Methods in pal.treesearch that return Tree
 Tree TreeSearchTool.basicUnrootedTreeMLSearch(Alignment a, SubstitutionModel sm, boolean optimiseModel)
          Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting tree
 Tree TreeSearchTool.basicUnrootedTreeMLSearch(Alignment a, SubstitutionModel sm, boolean optimiseModel, AlgorithmCallback callback)
          Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting tree
 Tree TreeSearchTool.basicUnrootedTreeMLSearch(Tree baseTree, Alignment a, SubstitutionModel sm, boolean optimiseModel)
          Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting tree
 Tree TreeSearchTool.basicUnrootedTreeMLSearch(Tree baseTree, Alignment a, SubstitutionModel sm, boolean optimiseModel, AlgorithmCallback callback)
          Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting tree
 Tree UnrootedMLSearcher.buildPALTree()
           
 Tree GeneralLikelihoodSearcher.buildPALTreeBase()
           
 Tree GeneralLikelihoodSearcher.buildPALTreeES()
           
static Tree TreeSearchTool.optimiseClockConstrainedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel, AlgorithmCallback callback)
          Optimise the branches of a tree with regard to maximum likelihood, with the contraints of a global molecular clock - that is, all the tips terminate at the same point.
static Tree TreeSearchTool.optimiseUnrootedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel)
          Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).
static Tree TreeSearchTool.optimiseUnrootedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel, AlgorithmCallback callback)
          Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).
 

Methods in pal.treesearch with parameters of type Tree
 Tree TreeSearchTool.basicUnrootedTreeMLSearch(Tree baseTree, Alignment a, SubstitutionModel sm, boolean optimiseModel)
          Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting tree
 Tree TreeSearchTool.basicUnrootedTreeMLSearch(Tree baseTree, Alignment a, SubstitutionModel sm, boolean optimiseModel, AlgorithmCallback callback)
          Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting tree
static double TreeSearchTool.calculateLogLikelihood(Tree tree, Alignment alignment, SubstitutionModel model)
          Calculate the log likelihood of a particular set of phylogenetic data
static Tree TreeSearchTool.optimiseClockConstrainedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel, AlgorithmCallback callback)
          Optimise the branches of a tree with regard to maximum likelihood, with the contraints of a global molecular clock - that is, all the tips terminate at the same point.
static Tree TreeSearchTool.optimiseUnrootedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel)
          Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).
static Tree TreeSearchTool.optimiseUnrootedFixed(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel, AlgorithmCallback callback)
          Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).
 

Constructors in pal.treesearch with parameters of type Tree
UnrootedMLSearcher(Tree t, Alignment alignment, SubstitutionModel model)
           
 

Uses of Tree in pal.xml
 

Methods in pal.xml that return Tree
static Tree ElementParser.parseTreeElement(org.w3c.dom.Element e)
           
 

Methods in pal.xml with parameters of type Tree
static org.w3c.dom.Element ElementFactory.createTreeElement(Tree tree, org.w3c.dom.Document document, boolean includeEdges)