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Packages that use Tree | |
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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 |
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Classes in pal.coalescent that implement Tree | |
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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 | |
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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 | |
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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 | |
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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. |
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SerialCoalescentGenerator.Results(Tree[] trees)
|
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SerialCoalescentGenerator.Results(Tree[] trees,
Alignment[] alignments)
|
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SkylinePlot(Tree tree,
double epsilon)
Construct skyline plot from tree |
Uses of Tree in pal.distance |
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Methods in pal.distance with parameters of type Tree | |
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static DistanceMatrixGenerator |
DistanceMatrixGenerator.Utils.createParametric(Tree baseTree,
SubstitutionModel sm,
int numberOfSites)
Silly idea stuff |
Uses of Tree in pal.eval |
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Methods in pal.eval that return Tree | |
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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 | |
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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 | |
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FastLikelihoodCalculator(SitePattern pattern,
Tree tree,
RateMatrix model)
Constructor taking site pattern, tree and model. |
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GeneralLikelihoodCalculator(Alignment baseAlignment,
Tree tree,
RateMatrix model)
Constructor taking site pattern, tree and a rate matrix. |
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GeneralLikelihoodCalculator(Alignment baseAlignment,
Tree tree,
RateMatrix model,
RateDistribution distribution)
Constructor taking site pattern, tree rate matrix, and a rate distribution |
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GeneralLikelihoodCalculator(Alignment baseAlignment,
Tree tree,
SubstitutionModel model)
Constructor taking site pattern, tree and a general substitution model. |
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LikelihoodOptimiser(Tree tree,
Alignment alignment,
SubstitutionModel model)
|
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SimpleLikelihoodCalculator(SitePattern pattern,
Tree tree,
RateMatrix model)
|
Uses of Tree in pal.gui |
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Methods in pal.gui that return Tree | |
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protected Tree |
TreePainter.getTree()
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Methods in pal.gui with parameters of type Tree | |
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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 | |
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TreeComponent(Tree tree)
|
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TreeComponent(Tree tree,
boolean usingSymbols)
|
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TreeComponent(Tree tree,
java.lang.String title)
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TreeComponent(Tree tree,
java.lang.String title,
boolean showTitle)
|
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TreeComponent(Tree tree,
TimeOrderCharacterData tocd,
boolean usingSymbols)
|
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TreePainter(Tree toDisplay,
java.lang.String title,
boolean showTitle)
|
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TreePainterCircular(Tree toDisplay,
java.lang.String title,
boolean showTitle)
|
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TreePainterNormal(Tree toDisplay,
java.lang.String title,
boolean showTitle)
|
Uses of Tree in pal.mep |
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Methods in pal.mep that return Tree | |
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Tree |
DeltaModel.Instance.generateAlternativeRepresentation(Tree expectedSubstitutionsTree)
|
Methods in pal.mep with parameters of type Tree | |
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Tree |
DeltaModel.Instance.generateAlternativeRepresentation(Tree expectedSubstitutionsTree)
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Uses of Tree in pal.statistics |
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Methods in pal.statistics that return Tree | |
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Tree |
LikelihoodEvaluator.MLResult.getOptimisedTree()
|
Tree |
LikelihoodEvaluator.SimpleMLResult.getOptimisedTree()
|
Tree[] |
GeneralTopologyPool.getOriginalOptimisedTrees()
|
Methods in pal.statistics with parameters of type Tree | |
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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 | |
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GeneralTopologyPool(Tree[] topologies,
LikelihoodEvaluator baseCalculator,
ReplicateLikelihoodEvaluator replicateCalculator,
Alignment baseAlignment,
AlignmentGenerator replicateGenerator)
|
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LikelihoodEvaluator.SimpleMLResult(double logLikelihood,
Tree optimisedTree)
|
Uses of Tree in pal.supgma |
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Classes in pal.supgma that implement Tree | |
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class |
SUPGMATree
constructs an SUPGMA tree from pairwise distances. |
Methods in pal.supgma that return Tree | |
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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 |
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Subinterfaces of Tree in pal.tree | |
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interface |
ParameterizedTree
abstract base class for a tree with an Parameterized interface |
Classes in pal.tree that implement Tree | |
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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 | |
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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 | |
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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 | |
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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)
|
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SimpleTree(Tree tree)
clone constructor |
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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 |
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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 |
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Methods in pal.treesearch that return Tree | |
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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 | |
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UnrootedMLSearcher(Tree t,
Alignment alignment,
SubstitutionModel model)
|
Uses of Tree in pal.xml |
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Methods in pal.xml that return Tree | |
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static Tree |
ElementParser.parseTreeElement(org.w3c.dom.Element e)
|
Methods in pal.xml with parameters of type Tree | |
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static org.w3c.dom.Element |
ElementFactory.createTreeElement(Tree tree,
org.w3c.dom.Document document,
boolean includeEdges)
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