Uses of Interface
pal.tree.Tree
Packages that use Tree
Package
Description
Classes to model population genetic processes using the coalescent.
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
GUI components for some special objects (e.g., trees).
Classes for the analysis of "measurably evolving populations" (mep).
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.)
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
Utility classes for converting PAL objects to and from XML documents.
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Uses of Tree in pal.coalescent
Classes in pal.coalescent that implement TreeModifier and TypeClassDescriptionclass
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 TreeModifier and TypeMethodDescriptionfinal Tree
SerialCoalescentGenerator.generateTree()
final Tree[]
SerialCoalescentGenerator.generateTrees
(AlgorithmCallback callback) If callback request stop then returns trees creating thus farSerialCoalescentSimulator.getTree()
final Tree[]
SerialCoalescentGenerator.Results.getTrees()
Methods in pal.coalescent with parameters of type TreeModifier and TypeMethodDescriptionstatic 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 TreeModifierConstructorDescriptionDemographicClockTree
(Tree t, DemographicModel model) take any tree and afford it with an interface suitable for a clock-like genealogy, under a certain demographic assumption.SkylinePlot
(Tree tree, double epsilon) Construct skyline plot from tree -
Uses of Tree in pal.distance
Methods in pal.distance with parameters of type TreeModifier and TypeMethodDescriptionstatic DistanceMatrixGenerator
DistanceMatrixGenerator.Utils.createParametric
(Tree baseTree, SubstitutionModel sm, int numberOfSites) Silly idea stuff -
Uses of Tree in pal.eval
Modifier and TypeMethodDescriptionChiSquareValue.getTree()
Returns the (parameterized) tree of this likelihood value.LikelihoodValue.getTree()
Returns the (potentially parameterized) tree of this likelihood value.SimpleLikelihoodCalculator.getTree()
static final 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 final 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 final 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 final 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 final 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).Modifier and TypeMethodDescriptionstatic final double
LikelihoodTool.calculateLogLikelihood
(Tree tree, Alignment alignment, SubstitutionModel model) Calculate the log likelihood of a particular set of phylogenetic datastatic final 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 final 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 final 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 final 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 final 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 final 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
define (parameterized) treefinal void
void
define (parameterized) tree ,(must only be called only after a site pattern has been defined).void
define tree ,(must only be called only after a site pattern has been defined).final void
GeneralLikelihoodCalculator.setup
(Tree t, SubstitutionModel model) ModifierConstructorDescriptionFastLikelihoodCalculator
(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 distributionGeneralLikelihoodCalculator
(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
Modifier and TypeMethodDescriptionvoid
final void
void
TreePainter.setTreeImpl
(Tree tree) may be implemented by sub classesvoid
TreePainterCircular.setTreeImpl
(Tree t) ModifierConstructorDescriptionTreeComponent
(Tree tree) TreeComponent
(Tree tree, boolean usingSymbols) TreeComponent
(Tree tree, String title) TreeComponent
(Tree tree, String title, boolean showTitle) TreeComponent
(Tree tree, TimeOrderCharacterData tocd, boolean usingSymbols) TreePainter
(Tree toDisplay, String title, boolean showTitle) TreePainterCircular
(Tree toDisplay, String title, boolean showTitle) TreePainterNormal
(Tree toDisplay, String title, boolean showTitle) -
Uses of Tree in pal.mep
Modifier and TypeMethodDescriptionDeltaModel.Instance.generateAlternativeRepresentation
(Tree expectedSubstitutionsTree) Modifier and TypeMethodDescriptionDeltaModel.Instance.generateAlternativeRepresentation
(Tree expectedSubstitutionsTree) -
Uses of Tree in pal.statistics
Methods in pal.statistics that return TreeModifier and TypeMethodDescriptionLikelihoodEvaluator.MLResult.getOptimisedTree()
LikelihoodEvaluator.SimpleMLResult.getOptimisedTree()
Tree[]
GeneralTopologyPool.getOriginalOptimisedTrees()
Methods in pal.statistics with parameters of type TreeModifier and TypeMethodDescriptiondouble
LikelihoodEvaluator.calculateLikelihood
(Tree tree, Alignment alignment) LikelihoodEvaluator.getMLOptimised
(Tree tree, Alignment alignment, AlgorithmCallback callback) double
ReplicateLikelihoodEvaluator.getReplicateLogLikelihood
(Tree tree, Alignment alignment) Constructors in pal.statistics with parameters of type TreeModifierConstructorDescriptionGeneralTopologyPool
(Tree[] topologies, LikelihoodEvaluator baseCalculator, ReplicateLikelihoodEvaluator replicateCalculator, Alignment baseAlignment, AlignmentGenerator replicateGenerator) SimpleMLResult
(double logLikelihood, Tree optimisedTree) -
Uses of Tree in pal.supgma
Classes in pal.supgma that implement TreeModifier and TypeClassDescriptionclass
constructs an SUPGMA tree from pairwise distances.Methods in pal.supgma that return TreeModifier and TypeMethodDescriptionSUPGMABase.generateAlignmentBootstrappedSUPGMATree
(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, SUPGMABase.PopulationParameters pp, int numberOfReplicates, LMSSolver solver) SUPGMABase.PopulationParameters.generateSUPGMATree
(ClusterTree.ClusteringMethod cm) SUPGMABase.PopulationParameters.generateSUPGMATree
(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, DistanceMatrixGenerator replicateSource, int numberOfAlignmentBootstrapReplicates, LMSSolver solver) SUPGMABase.PopulationParameters.simulateTree()
Tree[]
SUPGMABase.PopulationParameters.simulateTrees
(int numberOfTreesToSimulate, AlgorithmCallback callback, LMSSolver solver) SUPGMABase.solve
(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, LMSSolver solver) -
Uses of Tree in pal.tree
Modifier and TypeInterfaceDescriptioninterface
abstract base class for a tree with an Parameterized interfaceModifier and TypeClassDescriptionclass
provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)class
class
This class logarithmically transforms tree parameters.class
Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).class
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
For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)class
constructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted treesclass
data structure for a binary/non-binary rooted/unrooted treesstatic class
class
provides parameter interface to an unconstrained tree (parameters are all available branch lengths)class
Deprecated.Use ClusterTreeModifier and TypeMethodDescriptionstatic final Tree
TreeTool.createNeighbourJoiningTree
(double[][] dm, String[] otuNames) Neighbour-joining tree construction based on a distance matrixstatic final Tree
TreeTool.createNeighbourJoiningTree
(DistanceMatrix dm) Neighbour-joining tree construction based on a distance matrixstatic final Tree
TreeTool.createUPGMA
(DistanceMatrix dm) UPGMA tree construction based on a distance matrixstatic final Tree
TreeTool.createUPGMATree
(double[][] dm, String[] otuNames) UPGMA tree construction based on a distance matrixfinal 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 final Tree[]
TreeManipulator.getAllRootingsBy
(Tree base, String[] outgroupNames) Roots a tree by an outgroupTree[]
TreeManipulator.getAllTreesRootedBy
(String[] outgroupNames) TreeManipulator.getAsInputRootingTree()
A method for recovering the input (construction) tree (with the EXPANSION/MIMIC/REDUCED differences)protected Tree
ParameterizedTree.ParameterizedTreeBase.getBaseTree()
static final Tree
TreeUtils.getBootstrapSupportByCladeTree
(String attributeName, Tree baseTree, Tree[] alternativeTrees) Deprecated.Use getReplicateCladeSupport insteadClockTree.getCopy()
MutationRateModelTree.getCopy()
ParameterizedTree.ParameterizedTreeBase.getCopy()
The cheapy copy that just creates a SimpleTreeSimpleTree.getCopy()
Tree.getCopy()
UnconstrainedTree.getCopy()
TreeManipulator.getDefaultRootTree()
Tree[]
TreeManipulator.getEveryRoot()
static final Tree[]
TreeManipulator.getEveryRoot
(Tree base) Obtains every rooting of a base treestatic final Tree
TreeManipulator.getMidpointRooted
(Tree base) Returns the mid point rooting of a tree.static final Tree
TreeTool.getMidPointRooted
(Tree t) Root a tree around it's midpoint.TreeManipulator.getMidPointRootedTree()
TreeGenerator.getNextTree
(AlgorithmCallback callback) static final 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 identifiersstatic final Tree
TreeUtils.getReplicateCladeSupport
(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 final Tree
Root a tree by an outgroup.static final Tree
TreeManipulator.getRootedBy
(Tree base, String[] outgroupNames) Roots a tree by an outgroupstatic final Tree
TreeManipulator.getRootedBy
(Tree base, String[] outgroupNames, double ingroupBranchLength) Roots a tree by an outgroupstatic final Tree
Takes a tree and returns a scaled version of it.static final Tree
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.TreeManipulator.getTreeRootedAbove
(Node n) TreeManipulator.getTreeRootedBy
(String[] outgroupNames) TreeManipulator.getTreeRootedBy
(String[] outgroupNames, double ingroupBranchLength) static final Tree
TreeManipulator.getUnrooted
(Tree base) Unroots a treestatic final Tree
TreeTool.getUnrooted
(Tree t) Unroot a tree (makes the base of the tree a trification).TreeManipulator.getUnrootedTree()
return unrooted nodestatic Tree
static Tree
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).Operates on input tree.static final Tree
Read a tree from an input source.static Tree
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) Modifier and TypeMethodDescriptionstatic void
CladeSystem.calculateCladeProbabilities
(Tree tree, CladeSystem[] cladeSystems) static void
RootedTreeUtils.collectProportions
(Tree tree, Vector trees) static void
TreeUtils.computeAllDistances
(Tree tree, int a, double[] dist, double[] idist, boolean countEdges, double epsilon) static final double
TreeUtils.computeDistance
(Tree tree, int a, int b) compute distance between two external nodesstatic 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.final SimulatedAlignment
SimulatedAlignment.Factory.generateAlignment
(Tree tree) Generate a simulated alignment based on input treefinal SimulatedAlignment[]
SimulatedAlignment.Factory.generateAlignments
(Tree[] trees, AlgorithmCallback callback) Generate an array of simulated alignments based on an array of input treesParameterizedTree.Factory.generateNewTree
(Tree base) Generate a new parameterized tree wrapped around basestatic 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 final Tree[]
TreeManipulator.getAllRootingsBy
(Tree base, String[] outgroupNames) Roots a tree by an outgroupstatic final Tree
TreeUtils.getBootstrapSupportByCladeTree
(String attributeName, Tree baseTree, Tree[] alternativeTrees) Deprecated.Use getReplicateCladeSupport insteadstatic CladeSystem
creates a clade system from a tree (using a pre-specified order of sequences)static CladeSystem
creates a clade system from a tree (using tree-induced order of sequences)static CladeSystem[]
CladeSystem.getCladeSystems
(Tree[] trees) static final Tree[]
TreeManipulator.getEveryRoot
(Tree base) Obtains every rooting of a base treestatic final TreeIterator
TreeManipulator.getEveryRootIterator
(Tree base) Obtains every rooting of a base treestatic final IdGroup
TreeUtils.getLeafIdGroup
(Tree tree) get list of the identifiers of the external nodesstatic final Tree
TreeManipulator.getMidpointRooted
(Tree base) Returns the mid point rooting of a tree.static final Tree
TreeTool.getMidPointRooted
(Tree t) Root a tree around it's midpoint.static final Node
TreeUtils.getNodeByName
(Tree tree, String name) static final 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 identifiersstatic Node
TreeUtils.getRandomNode
(Tree tree) Returns a uniformly distributed random node from the tree, including both internal and external nodes.static final Tree
TreeUtils.getReplicateCladeSupport
(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 treesstatic double
TreeUtils.getRobinsonFouldsDistance
(Tree t1, Tree t2) computes Robinson-Foulds (1981) distance between two treesstatic double
TreeUtils.getRobinsonFouldsRescaledDistance
(SplitSystem s1, Tree t2) computes Robinson-Foulds (1981) distance between two trees rescaled to a number between 0 and 1static double
TreeUtils.getRobinsonFouldsRescaledDistance
(Tree t1, Tree t2) computes Robinson-Foulds (1981) distance between two trees rescaled to a number between 0 and 1static final Tree
Root a tree by an outgroup.static final Tree
TreeManipulator.getRootedBy
(Tree base, String[] outgroupNames) Roots a tree by an outgroupstatic final Tree
TreeManipulator.getRootedBy
(Tree base, String[] outgroupNames, double ingroupBranchLength) Roots a tree by an outgroupstatic final Tree
Takes a tree and returns a scaled version of it.static final Tree
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
creates a split system from a tree (using a pre-specified order of sequences)static SplitSystem
creates a split system from a tree (using tree-induced order of sequences)static final Tree
TreeManipulator.getUnrooted
(Tree base) Unroots a treestatic final Tree
TreeTool.getUnrooted
(Tree t) Unroot a tree (makes the base of the tree a trification).static final void
TreeUtils.labelInternalNodes
(Tree tree) Labels the internal nodes of the tree using numbers starting from 0.static Tree
static Tree
This method does a local interchange on the given tree: Note the original tree is modified.static final 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).Operates on input tree.static void
Local.print4TaxonTree
(Tree tree, PrintWriter out) static void
TreeUtils.printNH
(Tree tree, PrintWriter out) print a this tree in New Hampshire format (including distances and internal labels)static void
TreeUtils.printNH
(Tree tree, PrintWriter out, boolean printLengths, boolean printInternalLabels) print this tree in New Hampshire formatvoid
static void
TreeUtils.renameNodes
(Tree tree, 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, PrintWriter out) static void
static void
TreeUtils.rotateByLeafCount
(Tree tree) Rotates branches by leaf count.static Tree
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) ModifierConstructorDescriptiontake 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).ParameterizedTreeBase
(Tree baseTree) SimpleTree
(Tree tree) clone constructorSimpleTree
(Tree tree, boolean keepIdentifiers) clone constructorSimpleTree
(Tree tree, LabelMapping lm) clone constructorSimulatedAlignment
(int sites, Tree t, SubstitutionModel m) Inititalisationcompute 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 lengthsTreeDistanceMatrix
(Tree t, IdGroup idGroup, boolean countEdges, double epsilon) compute induced distance matrixTreeManipulator
(Tree base) Construct a TreeManipulator based around a normal treeTreeManipulator
(Tree base, int constructionMode) Construct a TreeManipulator based around a normal treeTreeRestricter
(Tree t, String[] names, boolean inclusion) 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 TreeModifier and TypeMethodDescriptionTreeSearchTool.basicUnrootedTreeMLSearch
(Alignment a, SubstitutionModel sm, boolean optimiseModel) Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting treeTreeSearchTool.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 treeTreeSearchTool.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 treeTreeSearchTool.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 treeUnrootedMLSearcher.buildPALTree()
GeneralLikelihoodSearcher.buildPALTreeBase()
GeneralLikelihoodSearcher.buildPALTreeES()
static final 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 final 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 final 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 TreeModifier and TypeMethodDescriptionTreeSearchTool.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 treeTreeSearchTool.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 treestatic final double
TreeSearchTool.calculateLogLikelihood
(Tree tree, Alignment alignment, SubstitutionModel model) Calculate the log likelihood of a particular set of phylogenetic datastatic final 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 final 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 final 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 TreeModifierConstructorDescriptionUnrootedMLSearcher
(Tree t, Alignment alignment, SubstitutionModel model) -
Uses of Tree in pal.xml
Modifier and TypeMethodDescriptionstatic Element
ElementFactory.createTreeElement
(Tree tree, Document document, boolean includeEdges)