# Uses of Interface
jebl.evolution.trees.RootedTree

Packages that use RootedTree
Package
Description
jebl.evolution.align
Provides classes and interfaces for pairwise alignment of two sequences.
jebl.evolution.coalescent
jebl.evolution.treemetrics
jebl.evolution.trees
jebl.evolution.treesimulation

## Uses of RootedTree in jebl.evolution.align

Methods in jebl.evolution.align with parameters of type RootedTree
Modifier and Type
Method
Description
`Alignment`
BartonSternberg.`doAlign(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)`
`Alignment`
MultipleAligner.`doAlign(List<Sequence> seqs, RootedTree guideTree, ProgressListener progress)`

## Uses of RootedTree in jebl.evolution.coalescent

Constructors in jebl.evolution.coalescent with parameters of type RootedTree
Modifier
Constructor
Description
``
`Coalescent(RootedTree tree, DemographicFunction demographicFunction)`
``
`Intervals(RootedTree tree)`

## Uses of RootedTree in jebl.evolution.treemetrics

Methods in jebl.evolution.treemetrics with parameters of type RootedTree
Modifier and Type
Method
Description
`double`
BilleraMetric.`getMetric(RootedTree tree1, RootedTree tree2)`
`double`
CladeHeightMetric.`getMetric(RootedTree tree1, RootedTree tree2)`
`double`
RobinsonsFouldMetric.`getMetric(RootedTree tree1, RootedTree tree2)`
`double`
RootedTreeMetric.`getMetric(RootedTree tree1, RootedTree tree2)`
calculates the metric between two rooted trees

## Uses of RootedTree in jebl.evolution.trees

Classes in jebl.evolution.trees that implement RootedTree
Modifier and Type
Class
Description
`class`
`AbstractRootedTree`
`class`
`CompactRootedTree`
A memory efficient rooted tree.
`class`
`FilteredRootedTree`
`class`
`MutableRootedTree`
A simple rooted tree providing some ability to manipulate the tree.
`final class`
`ReRootedTree`
A rooted tree concrete class that wraps another tree and provides a differently rooted view of that tree.
`class`
`RootedFromUnrooted`
Root an unrooted tree.
`final class`
`RootedSubtree`
A simple, immutable rooted tree implementation that is a subtree of an existing tree subtending a specified set of taxa..
`final class`
`SimpleRootedTree`
A simple, and initially immutable rooted tree implementation.
`class`
`SortedRootedTree`
`class`
`TransformedRootedTree`
This RootedTree class wraps another RootedTree and transforms the branch lengths and node heights using various functions.
Methods in jebl.evolution.trees that return RootedTree
Modifier and Type
Method
Description
`static RootedTree`
Utils.`copyTree(RootedTree treeToCopy)`
This method creates an unattached copy of the given rooted tree such that changes to the copied tree do not affect the original tree.
`RootedTree`
FilteredRootedTree.`getSource()`
`static RootedTree`
Utils.`rootTheTree(Tree tree)`
Return a rooted tree from any tree.
`static RootedTree`
ReRootedTree.`rootTreeAtCenter(RootedTree tree)`
Root any tree by locating the "center" of tree and adding a new root node at that point
`static RootedTree`
Utils.`rootTreeAtCenter(Tree tree)`
Root any tree by locating the "center" of tree and adding a new root node at that point
Methods in jebl.evolution.trees with parameters of type RootedTree
Modifier and Type
Method
Description
`void`
CladeSystem.`add(RootedTree tree)`
adds all the clades in the tree
`void`
CalculateSplitRates.`addTreeToDensityMap(jebl.evolution.trees.CalculateSplitRates.DensityMap densityMap, RootedTree tree)`
`static ConsensusTreeBuilder`
TreeBuilderFactory.`buildRooted(RootedTree[] trees, double supportThreshold, TreeBuilderFactory.ConsensusMethod method)`
`static RootedTree`
Utils.`copyTree(RootedTree treeToCopy)`
This method creates an unattached copy of the given rooted tree such that changes to the copied tree do not affect the original tree.
`static Comparator<Node>`
Utils.`createNodeDensityComparator(RootedTree tree)`
`static Comparator<Node>`
Utils.`createNodeDensityMinNodeHeightComparator(RootedTree tree)`
`Node`
ReRootedTree.`createNodes(RootedTree tree, Node parent, Node child)`
Clones the entire tree structure from the given (unrooted) Tree.
`Node`
SimpleRootedTree.`createNodes(RootedTree tree, Node node)`
Clones the entire tree structure from the given RootedTree.
`static String`
Utils.`DEBUGsubTreeRep(RootedTree tree, Node node)`
`static boolean`
RootedTreeUtils.`equal(RootedTree tree1, RootedTree tree2)`
Compares 2 trees and returns true if they have the same topology.
`static double`
RootedTreeUtils.`getAverageTipDistance(RootedTree tree, Node node)`
returns the average distance from the given node to all the tips below it
`static Node`
RootedTreeUtils.`getCommonAncestorNode(RootedTree tree, Set<Node> tipNodes)`
Gets the most recent common ancestor (MRCA) node of a set of tip nodes.
`static Set<Node>`
RootedTreeUtils.`getDescendantTips(RootedTree tree, Node node)`
Gets a set of tip nodes descended from the given node.
`static int`
Utils.`getExternalNodeCount(RootedTree tree, Node node)`
Return the number of external nodes under this node.
`static double`
Utils.`getLength(RootedTree tree)`
`static double`
RootedTreeUtils.`getMaxTipHeight(RootedTree tree, Node node)`
`static double`
Utils.`getMinNodeHeight(RootedTree tree, Node node)`
`static double`
RootedTreeUtils.`getMinTipHeight(RootedTree tree, Node node)`
`static List<Node>`
Utils.`getNodes(RootedTree tree, Node node)`
All nodes in subtree - parents before children (pre - order).
`static final int`
RootedTreeUtils.`getTipCount(RootedTree tree, Node node)`
Return the number of leaves under this node.
`static Set<Node>`
RootedTreeUtils.`getTipsForTaxa(RootedTree tree, Collection<Taxon> taxa)`
Gets a set of external nodes that correspond to the given taxa.
`static boolean`
RootedTreeUtils.`isBinary(RootedTree tree)`
`static boolean`
Utils.`isBinary(RootedTree rootedTree)`
`static boolean`
RootedTreeUtils.`isMonophyletic(RootedTree tree, Set<Node> tipNodes)`
Performs the a monophyly test on a set of tip nodes.
`static boolean`
RootedTreeUtils.`isUltrametric(RootedTree tree, double tolerance)`
`static boolean`
Utils.`isUltrametric(RootedTree rootedTree)`
`static Node`
Utils.`leftNb(RootedTree tree, Node node)`
Left Neighbour of a tip (taxon).
`static int`
Utils.`maxLevels(RootedTree tree)`
`static Node`
Utils.`rightNb(RootedTree tree, Node tipNode)`
Right Neighbour of a tip (taxon).
`static RootedTree`
ReRootedTree.`rootTreeAtCenter(RootedTree tree)`
Root any tree by locating the "center" of tree and adding a new root node at that point
`static double`
Utils.`safeNodeHeight(RootedTree tree, Node node)`
`static String`
Utils.`toNewick(RootedTree tree)`
`static String`
Utils.`toUniqueNewick(RootedTree tree)`
Constructs a unique newick representation of a tree
`static String`
Utils.`toUniqueNewickByAttribute(RootedTree tree, String attribute)`
Constructs a unique newick representation of a tree print only an attribute
`static String`
RootedTreeUtils.`uniqueNewick(RootedTree tree, Node node)`
Recursive function for constructing a newick tree representation in the given buffer.
Constructors in jebl.evolution.trees with parameters of type RootedTree
Modifier
Constructor
Description
``
`AttributedCladeSystem(String name, RootedTree tree)`
``
`CladeSystem(RootedTree tree)`
``
`CompactRootedTree(RootedTree t)`
Do all the hard work.
``
`FilteredRootedTree(RootedTree source)`
``
`MutableRootedTree(RootedTree tree)`
Construct a rooted tree from an immutable rooted tree.
``
`ReRootedTree(RootedTree source, Node ingroupNode, Node outgroupNode, double ingroupBranchLength)`
Make a copy of the given unrooted tree
``
`RootedSubtree(RootedTree tree, Set<Taxon> includedTaxa)`
Make a copy of the given rooted tree
``
`SimpleRootedTree(RootedTree tree)`
Make a copy of the given rooted tree
``
`SimpleRootedTree(RootedTree tree, Map<Node,Node> nodeMapping)`
Make a copy of the given rooted tree
``
`SortedRootedTree(RootedTree source, Comparator<Node> comparator)`
``
`SortedRootedTree(RootedTree source, SortedRootedTree.BranchOrdering branchOrdering)`
``
`TransformedRootedTree(RootedTree source, TransformedRootedTree.Transform transform)`
``
`TreeBiPartitionInfo(RootedTree t, List<Taxon> taxa)`

## Uses of RootedTree in jebl.evolution.treesimulation

Methods in jebl.evolution.treesimulation that return RootedTree
Modifier and Type
Method
Description
`RootedTree`
TreeSimulator.`simulate(IntervalGenerator intervalGenerator)`
`RootedTree`
TreeSimulator.`simulate(IntervalGenerator intervalGenerator, boolean medianHeights)`