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.
|
Modifier and Type | Class and 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).
|
Modifier and Type | Method and Description |
---|---|
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() |
Modifier and Type | Method and 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.
|
Constructor and 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
|
Modifier and Type | Method and Description |
---|---|
static DistanceMatrixGenerator |
DistanceMatrixGenerator.Utils.createParametric(Tree baseTree,
SubstitutionModel sm,
int numberOfSites)
Silly idea stuff
|
Modifier and Type | Method and Description |
---|---|
Tree |
LikelihoodValue.getTree()
Returns the (potentially parameterized) tree of this likelihood value.
|
Tree |
ChiSquareValue.getTree()
Returns the (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).
|
Modifier and Type | Method and Description |
---|---|
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 |
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 |
ChiSquareValue.setTree(Tree t)
define (parameterized) tree
|
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) |
Constructor and 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 distribution
|
GeneralLikelihoodCalculator(Alignment baseAlignment,
Tree tree,
SubstitutionModel model)
Constructor taking site pattern, tree and a general substitution model.
|
LikelihoodOptimiser(Tree tree,
Alignment alignment,
SubstitutionModel model) |
SimpleLikelihoodCalculator(SitePattern pattern,
Tree tree,
RateMatrix model) |
Modifier and Type | Method and Description |
---|---|
protected Tree |
TreePainter.getTree() |
Modifier and Type | Method and Description |
---|---|
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) |
Constructor and 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) |
Modifier and Type | Method and Description |
---|---|
Tree |
DeltaModel.Instance.generateAlternativeRepresentation(Tree expectedSubstitutionsTree) |
Modifier and Type | Method and Description |
---|---|
Tree |
DeltaModel.Instance.generateAlternativeRepresentation(Tree expectedSubstitutionsTree) |
Modifier and Type | Method and Description |
---|---|
Tree |
LikelihoodEvaluator.MLResult.getOptimisedTree() |
Tree |
LikelihoodEvaluator.SimpleMLResult.getOptimisedTree() |
Tree[] |
GeneralTopologyPool.getOriginalOptimisedTrees() |
Modifier and Type | Method and 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) |
Constructor and Description |
---|
GeneralTopologyPool(Tree[] topologies,
LikelihoodEvaluator baseCalculator,
ReplicateLikelihoodEvaluator replicateCalculator,
Alignment baseAlignment,
AlignmentGenerator replicateGenerator) |
SimpleMLResult(double logLikelihood,
Tree optimisedTree) |
Modifier and Type | Class and Description |
---|---|
class |
SUPGMATree
constructs an SUPGMA tree from pairwise distances.
|
Modifier and Type | Method and Description |
---|---|
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) |
Modifier and Type | Interface and Description |
---|---|
interface |
ParameterizedTree
abstract base class for a tree with an Parameterized interface
|
Modifier and Type | Class and 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 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
|
Modifier and Type | Method and Description |
---|---|
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 |
ParameterizedTree.ParameterizedTreeBase.getCopy()
The cheapy copy that just creates a SimpleTree
|
Tree |
ClockTree.getCopy() |
Tree |
Tree.getCopy() |
Tree |
UnconstrainedTree.getCopy() |
Tree |
MutationRateModelTree.getCopy() |
Tree |
SimpleTree.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 |
TreeManipulator.getUnrooted(Tree base)
Unroots a tree
|
static Tree |
TreeTool.getUnrooted(Tree t)
Unroot a tree (makes the base of the tree a trification).
|
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) |
Modifier and Type | Method and 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 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 |
TreeManipulator.getUnrooted(Tree base)
Unroots a tree
|
static 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 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) |
Constructor and Description |
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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).
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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).
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ParameterizedTreeBase(Tree baseTree) |
SimpleTree(Tree tree)
clone constructor
|
SimpleTree(Tree tree,
boolean keepIdentifiers)
clone constructor
|
SimpleTree(Tree tree,
LabelMapping lm)
clone constructor
|
SimulatedAlignment(int sites,
Tree t,
SubstitutionModel m)
Inititalisation
|
TreeDistanceMatrix(Tree t)
compute induced distance matrix using actual branch lengths
(using tree-induced order of sequences)
|
TreeDistanceMatrix(Tree t,
boolean countEdges,
double epsilon)
compute induced distance matrix
(using tree-induced order of sequences)
|
TreeDistanceMatrix(Tree t,
IdGroup idGroup)
compute induced distance matrix using actual branch lengths
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TreeDistanceMatrix(Tree t,
IdGroup idGroup,
boolean countEdges,
double epsilon)
compute induced distance matrix
|
TreeManipulator(Tree base)
Construct a TreeManipulator based around a normal tree
|
TreeManipulator(Tree base,
int constructionMode)
Construct a TreeManipulator based around a normal tree
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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)
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Modifier and Type | Method and Description |
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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).
|
Modifier and Type | Method and 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 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).
|
Constructor and Description |
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UnrootedMLSearcher(Tree t,
Alignment alignment,
SubstitutionModel model) |
Modifier and Type | Method and Description |
---|---|
static Tree |
ElementParser.parseTreeElement(org.w3c.dom.Element e) |
Modifier and Type | Method and Description |
---|---|
static org.w3c.dom.Element |
ElementFactory.createTreeElement(Tree tree,
org.w3c.dom.Document document,
boolean includeEdges) |