Contains methods to generate random trees. More...

Static Public Member Functions
static TreeNode	UnlabelledTopology (int leafCount, TreeNode.NullHypothesis model=TreeNode.NullHypothesis.PDA, bool rooted=false)
	Samples a random unlabelled topology according to the specified model. More...

static TreeNode	UnlabelledTree (int leafCount, IContinuousDistribution branchLengthDistribution, TreeNode.NullHypothesis model=TreeNode.NullHypothesis.PDA, bool rooted=false)
	Samples a random unlabelled tree according to the specified model, using branch lengths drawn from the supplied distribution. More...

static TreeNode	UnlabelledTree (int leafCount, TreeNode.NullHypothesis model=TreeNode.NullHypothesis.PDA, bool rooted=false)
	Samples a random unlabelled tree according to the specified model, using branch lengths drawn from a Uniform(0, 1) distribution. More...

static TreeNode	ResolvePolytomies (TreeNode tree, bool rooted=false)
	Randomly resolve all the polytomies in a tree. More...

static TreeNode	LabelledTopology (IReadOnlyList< string > leafNames, TreeNode.NullHypothesis model=TreeNode.NullHypothesis.PDA, bool rooted=false, TreeNode constraint=null)
	Samples a random labelled topology according to the specified model. More...

static TreeNode	LabelledTopology (int leafCount, TreeNode.NullHypothesis model=TreeNode.NullHypothesis.PDA, bool rooted=false, TreeNode constraint=null)
	Samples a random labelled topology according to the specified model. More...

static TreeNode	LabelledTree (IReadOnlyList< string > leafNames, IContinuousDistribution branchLengthDistribution, TreeNode.NullHypothesis model=TreeNode.NullHypothesis.PDA, bool rooted=false, TreeNode constraint=null)
	Samples a random labelled tree according to the specified model, using branch lengths drawn from the supplied distribution. More...

static TreeNode	LabelledTree (int leafCount, IContinuousDistribution branchLengthDistribution, TreeNode.NullHypothesis model=TreeNode.NullHypothesis.PDA, bool rooted=false, TreeNode constraint=null)
	Samples a random labelled tree according to the specified model, using branch lengths drawn from the supplied distribution. More...

static TreeNode	LabelledTree (IReadOnlyList< string > leafNames, TreeNode.NullHypothesis model=TreeNode.NullHypothesis.PDA, bool rooted=false, TreeNode constraint=null)
	Samples a random labelled tree according to the specified model, using branch lengths drawn from a Uniform(0, 1) distribution. More...

static TreeNode	LabelledTree (int leafCount, TreeNode.NullHypothesis model=TreeNode.NullHypothesis.PDA, bool rooted=false, TreeNode constraint=null)
	Samples a random labelled tree according to the specified model, using branch lengths drawn from a Uniform(0, 1) distribution. More...

Static Public Attributes
static Random	RandomNumberGenerator = new ThreadSafeRandom()
	Random number generator used for sampling. More...

Detailed Description

Contains methods to generate random trees.

Definition at line 12 of file RandomTree.cs.

Member Function Documentation

◆ LabelledTopology() [1/2]

static TreeNode PhyloTree.TreeBuilding.RandomTree.LabelledTopology	(	int	leafCount,
		TreeNode.NullHypothesis	model = `TreeNode.NullHypothesis.PDA`,
		bool	rooted = `false`,
		TreeNode	constraint = `null`
	)

static

Samples a random labelled topology according to the specified model.

Parameters

leafCount	The number of terminal nodes in the topology. Their names will be in the form `t1, t2, ..., tN`, where `N` is leafCount .
model	The model to use for growing the tree.
rooted	A bool indicating whether the tree should be rooted or not.
constraint	A tree to constrain the sampling. The topology produced by this method will be compatible with this tree. The constraint tree can be multifurcating. Please note that, as the constraint is applied at every step while growing the topology, using a constraint with TreeNode.NullHypothesis.YHK will bias the sampled topology distribution.

Returns: A TreeNode object containing a random labelled topology (branch lengths will all be set to double.NaN).

Exceptions

ArgumentException Thrown if model is neither TreeNode.NullHypothesis.PDA nor TreeNode.NullHypothesis.YHK.

Definition at line 535 of file RandomTree.cs.

◆ LabelledTopology() [2/2]

static TreeNode PhyloTree.TreeBuilding.RandomTree.LabelledTopology	(	IReadOnlyList< string >	leafNames,
		TreeNode.NullHypothesis	model = `TreeNode.NullHypothesis.PDA`,
		bool	rooted = `false`,
		TreeNode	constraint = `null`
	)

static

Samples a random labelled topology according to the specified model.

Parameters

leafNames	The labels for the terminal nodes of the topology.
model	The model to use for growing the tree.
rooted	A bool indicating whether the tree should be rooted or not.
constraint	A tree to constrain the sampling. The topology produced by this method will be compatible with this tree. The constraint tree can be multifurcating. Please note that, as the constraint is applied at every step while growing the topology, using a constraint with TreeNode.NullHypothesis.YHK will bias the sampled topology distribution.

Returns: A TreeNode object containing a random labelled topology (branch lengths will all be set to double.NaN).

Exceptions

ArgumentException Thrown if model is neither TreeNode.NullHypothesis.PDA nor TreeNode.NullHypothesis.YHK.

Definition at line 292 of file RandomTree.cs.

◆ LabelledTree() [1/4]

static TreeNode PhyloTree.TreeBuilding.RandomTree.LabelledTree	(	int	leafCount,
		IContinuousDistribution	branchLengthDistribution,
		TreeNode.NullHypothesis	model = `TreeNode.NullHypothesis.PDA`,
		bool	rooted = `false`,
		TreeNode	constraint = `null`
	)

static

Samples a random labelled tree according to the specified model, using branch lengths drawn from the supplied distribution.

Parameters

leafCount	The number of terminal nodes in the topology. Their names will be in the form `t1, t2, ..., tN`, where `N` is leafCount .
branchLengthDistribution	The continuous univariate distribution from which the branch lengths will be drawn.
model	The model to use for growing the tree.
rooted	A bool indicating whether the tree should be rooted or not.
constraint	A tree to constrain the sampling. The topology produced by this method will be compatible with this tree. The constraint tree can be multifurcating. Please note that, as the constraint is applied at every step while growing the topology, using a constraint with TreeNode.NullHypothesis.YHK will bias the sampled topology distribution.

Returns: A TreeNode object containing a random unlabelled tree, with branch lengths.

Definition at line 585 of file RandomTree.cs.

◆ LabelledTree() [2/4]

static TreeNode PhyloTree.TreeBuilding.RandomTree.LabelledTree	(	int	leafCount,
		TreeNode.NullHypothesis	model = `TreeNode.NullHypothesis.PDA`,
		bool	rooted = `false`,
		TreeNode	constraint = `null`
	)

static

Samples a random labelled tree according to the specified model, using branch lengths drawn from a Uniform(0, 1) distribution.

Parameters

leafCount	The number of terminal nodes in the topology. Their names will be in the form `t1, t2, ..., tN`, where `N` is leafCount .
model	The model to use for growing the tree.
rooted	A bool indicating whether the tree should be rooted or not.
constraint	A tree to constrain the sampling. The topology produced by this method will be compatible with this tree. The constraint tree can be multifurcating. Please note that, as the constraint is applied at every step while growing the topology, using a constraint with TreeNode.NullHypothesis.YHK will bias the sampled topology distribution.

Returns: A TreeNode object containing a random unlabelled tree, with branch lengths.

Definition at line 620 of file RandomTree.cs.

◆ LabelledTree() [3/4]

static TreeNode PhyloTree.TreeBuilding.RandomTree.LabelledTree	(	IReadOnlyList< string >	leafNames,
		IContinuousDistribution	branchLengthDistribution,
		TreeNode.NullHypothesis	model = `TreeNode.NullHypothesis.PDA`,
		bool	rooted = `false`,
		TreeNode	constraint = `null`
	)

static

Samples a random labelled tree according to the specified model, using branch lengths drawn from the supplied distribution.

Parameters

leafNames	The labels for the terminal nodes of the topology.
branchLengthDistribution	The continuous univariate distribution from which the branch lengths will be drawn.
model	The model to use for growing the tree.
rooted	A bool indicating whether the tree should be rooted or not.
constraint	A tree to constrain the sampling. The topology produced by this method will be compatible with this tree. The constraint tree can be multifurcating. Please note that, as the constraint is applied at every step while growing the topology, using a constraint with TreeNode.NullHypothesis.YHK will bias the sampled topology distribution.

Returns: A TreeNode object containing a random unlabelled tree, with branch lengths.

Definition at line 557 of file RandomTree.cs.

◆ LabelledTree() [4/4]

static TreeNode PhyloTree.TreeBuilding.RandomTree.LabelledTree	(	IReadOnlyList< string >	leafNames,
		TreeNode.NullHypothesis	model = `TreeNode.NullHypothesis.PDA`,
		bool	rooted = `false`,
		TreeNode	constraint = `null`
	)

static

Samples a random labelled tree according to the specified model, using branch lengths drawn from a Uniform(0, 1) distribution.

Parameters

leafNames	The labels for the terminal nodes of the topology.
model	The model to use for growing the tree.
rooted	A bool indicating whether the tree should be rooted or not.
constraint	A tree to constrain the sampling. The topology produced by this method will be compatible with this tree. The constraint tree can be multifurcating. Please note that, as the constraint is applied at every step while growing the topology, using a constraint with TreeNode.NullHypothesis.YHK will bias the sampled topology distribution.

Returns: A TreeNode object containing a random unlabelled tree, with branch lengths.

Definition at line 606 of file RandomTree.cs.

◆ ResolvePolytomies()

static TreeNode PhyloTree.TreeBuilding.RandomTree.ResolvePolytomies	(	TreeNode	tree,
		bool	rooted = `false`
	)

static

Randomly resolve all the polytomies in a tree.

Parameters

tree	The tree containing the polytomies to be resolved.
rooted	A bool indicating whether the tree is supposed to be rooted or not. If this is `true`, a trichotomy at the root node will be resolved.

Returns: The tree, where all the polytomies have been randomly resolved. This is performed in-place, but the return value of this method should be used in case the root node has changed.

Definition at line 217 of file RandomTree.cs.

◆ UnlabelledTopology()

static TreeNode PhyloTree.TreeBuilding.RandomTree.UnlabelledTopology	(	int	leafCount,
		TreeNode.NullHypothesis	model = `TreeNode.NullHypothesis.PDA`,
		bool	rooted = `false`
	)

static

Samples a random unlabelled topology according to the specified model.

Parameters

leafCount	The number of terminal nodes in the topology.
model	The model to use for growing the tree.
rooted	A bool indicating whether the tree should be rooted or not.

Returns: A TreeNode object containing a random unlabelled topology (branch lengths will all be set to double.NaN).

Exceptions

ArgumentException Thrown if model is neither TreeNode.NullHypothesis.PDA nor TreeNode.NullHypothesis.YHK.

Definition at line 27 of file RandomTree.cs.

◆ UnlabelledTree() [1/2]

static TreeNode PhyloTree.TreeBuilding.RandomTree.UnlabelledTree	(	int	leafCount,
		IContinuousDistribution	branchLengthDistribution,
		TreeNode.NullHypothesis	model = `TreeNode.NullHypothesis.PDA`,
		bool	rooted = `false`
	)

static

Samples a random unlabelled tree according to the specified model, using branch lengths drawn from the supplied distribution.

Parameters

leafCount	The number of terminal nodes in the topology.
branchLengthDistribution	The continuous univariate distribution from which the branch lengths will be drawn.
model	The model to use for growing the tree.
rooted	A bool indicating whether the tree should be rooted or not.

Returns: A TreeNode object containing a random unlabelled tree, with branch lengths.

Definition at line 150 of file RandomTree.cs.

◆ UnlabelledTree() [2/2]

static TreeNode PhyloTree.TreeBuilding.RandomTree.UnlabelledTree	(	int	leafCount,
		TreeNode.NullHypothesis	model = `TreeNode.NullHypothesis.PDA`,
		bool	rooted = `false`
	)

static

Samples a random unlabelled tree according to the specified model, using branch lengths drawn from a Uniform(0, 1) distribution.

Parameters

leafCount	The number of terminal nodes in the topology.
model	The model to use for growing the tree.
rooted	A bool indicating whether the tree should be rooted or not.

Returns: A TreeNode object containing a random unlabelled tree, with branch lengths.

Definition at line 175 of file RandomTree.cs.

Member Data Documentation

◆ RandomNumberGenerator

Random PhyloTree.TreeBuilding.RandomTree.RandomNumberGenerator = new ThreadSafeRandom()

static

Random number generator used for sampling.

Definition at line 17 of file RandomTree.cs.

The documentation for this class was generated from the following file:

TreeBuilding/RandomTree.cs

Static Public Member Functions

Static Public Attributes

Detailed Description

Member Function Documentation

◆ LabelledTopology() [1/2]

◆ LabelledTopology() [2/2]

◆ LabelledTree() [1/4]

◆ LabelledTree() [2/4]

◆ LabelledTree() [3/4]

◆ LabelledTree() [4/4]

◆ ResolvePolytomies()

◆ UnlabelledTopology()

◆ UnlabelledTree() [1/2]

◆ UnlabelledTree() [2/2]

Member Data Documentation

◆ RandomNumberGenerator