Uses of Interface
pal.tree.Tree
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Packages that use Tree Package Description 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. -
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Uses of Tree in pal.coalescent
Classes in pal.coalescent that implement Tree Modifier and Type Class Description 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 Modifier and Type Method Description Tree
SerialCoalescentGenerator. generateTree()
Tree[]
SerialCoalescentGenerator. generateTrees(AlgorithmCallback callback)
If callback request stop then returns trees creating thus farTree
SerialCoalescentSimulator. getTree()
Tree[]
SerialCoalescentGenerator.Results. getTrees()
Methods in pal.coalescent with parameters of type Tree Modifier and Type Method Description 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 Constructor Description 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.Results(Tree[] trees)
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 Modifier and Type Method Description 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 Modifier and Type Method Description Tree
ChiSquareValue. getTree()
Returns the (parameterized) tree of this likelihood value.Tree
LikelihoodValue. getTree()
Returns the (potentially parameterized) tree of this likelihood value.Tree
SimpleLikelihoodCalculator. getTree()
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 Modifier and Type Method Description static double
LikelihoodTool. calculateLogLikelihood(Tree tree, Alignment alignment, SubstitutionModel model)
Calculate the log likelihood of a particular set of phylogenetic datastatic 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) treevoid
FastLikelihoodCalculator. setTree(Tree t)
void
LikelihoodValue. setTree(Tree t)
define (parameterized) tree ,(must only be called only after a site pattern has been defined).void
SimpleLikelihoodCalculator. setTree(Tree t)
define 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 Constructor Description 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 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)
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Uses of Tree in pal.gui
Methods in pal.gui that return Tree Modifier and Type Method Description protected Tree
TreePainter. getTree()
Methods in pal.gui with parameters of type Tree Modifier and Type Method Description void
TreeComponent. setTree(Tree tree)
void
TreePainter. setTree(Tree tree)
void
TreePainter. setTreeImpl(Tree tree)
may be implemented by sub classesvoid
TreePainterCircular. setTreeImpl(Tree t)
Constructors in pal.gui with parameters of type Tree Constructor Description 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)
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Uses of Tree in pal.mep
Methods in pal.mep that return Tree Modifier and Type Method Description Tree
DeltaModel.Instance. generateAlternativeRepresentation(Tree expectedSubstitutionsTree)
Methods in pal.mep with parameters of type Tree Modifier and Type Method Description Tree
DeltaModel.Instance. generateAlternativeRepresentation(Tree expectedSubstitutionsTree)
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Uses of Tree in pal.statistics
Methods in pal.statistics that return Tree Modifier and Type Method Description Tree
LikelihoodEvaluator.MLResult. getOptimisedTree()
Tree
LikelihoodEvaluator.SimpleMLResult. getOptimisedTree()
Tree[]
GeneralTopologyPool. getOriginalOptimisedTrees()
Methods in pal.statistics with parameters of type Tree Modifier and Type Method Description 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 Constructor Description GeneralTopologyPool(Tree[] topologies, LikelihoodEvaluator baseCalculator, ReplicateLikelihoodEvaluator replicateCalculator, Alignment baseAlignment, AlignmentGenerator replicateGenerator)
SimpleMLResult(double logLikelihood, Tree optimisedTree)
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Uses of Tree in pal.supgma
Classes in pal.supgma that implement Tree Modifier and Type Class Description class
SUPGMATree
constructs an SUPGMA tree from pairwise distances.Methods in pal.supgma that return Tree Modifier and Type Method Description Tree
SUPGMABase. generateAlignmentBootstrappedSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, SUPGMABase.PopulationParameters pp, int numberOfReplicates, LMSSolver solver)
Tree
SUPGMABase.PopulationParameters. generateSUPGMATree(ClusterTree.ClusteringMethod cm)
Tree
SUPGMABase.PopulationParameters. generateSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, DistanceMatrixGenerator replicateSource, int numberOfAlignmentBootstrapReplicates, LMSSolver solver)
Tree
SUPGMABase.PopulationParameters. simulateTree()
Tree[]
SUPGMABase.PopulationParameters. simulateTrees(int numberOfTreesToSimulate, AlgorithmCallback callback, LMSSolver solver)
Tree
SUPGMABase. solve(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, LMSSolver solver)
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Uses of Tree in pal.tree
Subinterfaces of Tree in pal.tree Modifier and Type Interface Description interface
ParameterizedTree
abstract base class for a tree with an Parameterized interfaceClasses in pal.tree that implement Tree Modifier and Type Class Description 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 treesclass
SimpleTree
data structure for a binary/non-binary rooted/unrooted treesstatic class
Tree.TreeBase
class
UnconstrainedTree
provides parameter interface to an unconstrained tree (parameters are all available branch lengths)class
UPGMATree
Deprecated.Use ClusterTreeMethods in pal.tree that return Tree Modifier and Type Method Description static Tree
TreeTool. createNeighbourJoiningTree(double[][] dm, java.lang.String[] otuNames)
Neighbour-joining tree construction based on a distance matrixstatic Tree
TreeTool. createNeighbourJoiningTree(DistanceMatrix dm)
Neighbour-joining tree construction based on a distance matrixstatic Tree
TreeTool. createUPGMA(DistanceMatrix dm)
UPGMA tree construction based on a distance matrixstatic Tree
TreeTool. createUPGMATree(double[][] dm, java.lang.String[] otuNames)
UPGMA tree construction based on a distance matrixTree
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 outgroupTree[]
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 insteadTree
ClockTree. getCopy()
Tree
MutationRateModelTree. getCopy()
Tree
ParameterizedTree.ParameterizedTreeBase. getCopy()
The cheapy copy that just creates a SimpleTreeTree
SimpleTree. getCopy()
Tree
Tree. getCopy()
Tree
UnconstrainedTree. getCopy()
Tree
TreeManipulator. getDefaultRootTree()
Tree[]
TreeManipulator. getEveryRoot()
static Tree[]
TreeManipulator. getEveryRoot(Tree base)
Obtains every rooting of a base treestatic 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 identifiersstatic 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 outgroupstatic Tree
TreeManipulator. getRootedBy(Tree base, java.lang.String[] outgroupNames, double ingroupBranchLength)
Roots a tree by an outgroupstatic 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
TreeManipulator. getUnrooted(Tree base)
Unroots a treestatic Tree
TreeTool. getUnrooted(Tree t)
Unroot a tree (makes the base of the tree a trification).Tree
TreeManipulator. getUnrootedTree()
return unrooted nodestatic 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 Modifier and Type Method Description 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 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.SimulatedAlignment
SimulatedAlignment.Factory. generateAlignment(Tree tree)
Generate a simulated alignment based on input treeSimulatedAlignment[]
SimulatedAlignment.Factory. generateAlignments(Tree[] trees, AlgorithmCallback callback)
Generate an array of simulated alignments based on an array of input treesParameterizedTree
ParameterizedTree.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 Tree[]
TreeManipulator. getAllRootingsBy(Tree base, java.lang.String[] outgroupNames)
Roots a tree by an outgroupstatic Tree
TreeUtils. getBootstrapSupportByCladeTree(java.lang.String attributeName, Tree baseTree, Tree[] alternativeTrees)
Deprecated.Use getReplicateCladeSupport insteadstatic 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 treestatic TreeIterator
TreeManipulator. getEveryRootIterator(Tree base)
Obtains every rooting of a base treestatic IdGroup
TreeUtils. getLeafIdGroup(Tree tree)
get list of the identifiers of the external nodesstatic 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 identifiersstatic 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 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 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 outgroupstatic Tree
TreeManipulator. getRootedBy(Tree base, java.lang.String[] outgroupNames, double ingroupBranchLength)
Roots a tree by an outgroupstatic 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
TreeManipulator. getUnrooted(Tree base)
Unroots a treestatic Tree
TreeTool. getUnrooted(Tree t)
Unroot a tree (makes the base of the tree a trification).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 formatvoid
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 Constructor Description 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).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)
InititalisationTreeDistanceMatrix(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 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, 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 Modifier and Type Method Description 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 treeTree
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 treeTree
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 treeTree
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 treeTree
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 Modifier and Type Method Description 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 treeTree
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 treestatic double
TreeSearchTool. calculateLogLikelihood(Tree tree, Alignment alignment, SubstitutionModel model)
Calculate the log likelihood of a particular set of phylogenetic datastatic 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 Constructor Description UnrootedMLSearcher(Tree t, Alignment alignment, SubstitutionModel model)
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Uses of Tree in pal.xml
Methods in pal.xml that return Tree Modifier and Type Method Description static Tree
ElementParser. parseTreeElement(org.w3c.dom.Element e)
Methods in pal.xml with parameters of type Tree Modifier and Type Method Description static org.w3c.dom.Element
ElementFactory. createTreeElement(Tree tree, org.w3c.dom.Document document, boolean includeEdges)
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