Contains methods to simulate sequence evolution. More...

Public Member Functions
delegate double	GetScale (double conservation)
	Represents a function that can be evaluated to return the scaling factor to use in order to obtain the specified average conservation . More...

Static Public Member Functions
static Dictionary< string, Sequence >	SimulateSequences (this TreeNode tree, Sequence ancestralSequence, RateMatrix rateMatrix, double scale=1, IndelModel indelModel=null)
	Simulates the evolution of the specified ancestral sequence over a phylogenetic tree , with the specified rate matrix, scale factor, and insertion/deletion model. More...

static Dictionary< string, Sequence >	SimulateSequences (this TreeNode tree, int ancestralSequenceLength, RateMatrix rateMatrix, double scale=1, IndelModel indelModel=null)
	Simulates the evolution of a random ancestral sequence with the specified length over a phylogenetic tree , with the specified rate matrix, scale factor, and insertion/deletion model. More...

static Dictionary< string, Sequence >	SimulateAllSequences (this TreeNode tree, Sequence ancestralSequence, RateMatrix rateMatrix, double scale=1, IndelModel indelModel=null)
	Simulates the evolution of the specified ancestral sequence over a phylogenetic tree , with the specified rate matrix, scale factor, and insertion/deletion model. More...

static Dictionary< string, Sequence >	SimulateAllSequences (this TreeNode tree, int ancestralSequenceLength, RateMatrix rateMatrix, double scale=1, IndelModel indelModel=null)
	Simulates the evolution of a random ancestral sequence with the specified length over a phylogenetic tree , with the specified rate matrix, scale factor, and insertion/deletion model. More...

static GetScale	ConservationToScale (TreeNode tree, RateMatrix rateMatrix, double minRate=1e-5, double maxRate=1e4)
	Returns a method that can be evaluated to determine the scaling factor that, when applied to a sequence simulation done using the specified tree and rate matrix, will produce at the tips a sequence alignment with the specified (average) percent identity. More...

static Dictionary< string, string >	ToStringAlignment (this Dictionary< string, Sequence > alignment)
	Converts a sequence alignment where the sequences are stored as Sequences into an alignment where the sequences are stored as `string`s. More...

Properties
static Random	RandomNumberGenerator = new ThreadSafeRandom() `[get, set]`
	The random number generator used to simulate sequence evolution. If you change this, please ensure that it is thread-safe. More...

Detailed Description

Contains methods to simulate sequence evolution.

Definition at line 16 of file SequenceSimulation.cs.

Member Function Documentation

◆ ConservationToScale()

static GetScale PhyloTree.SequenceSimulation.SequenceSimulation.ConservationToScale	(	TreeNode	tree,
		RateMatrix	rateMatrix,
		double	minRate = `1e-5`,
		double	maxRate = `1e4`
	)

static

Returns a method that can be evaluated to determine the scaling factor that, when applied to a sequence simulation done using the specified tree and rate matrix, will produce at the tips a sequence alignment with the specified (average) percent identity.

Parameters

tree	The TreeNode on which the sequence simulations will be performed.
rateMatrix	The rate matrix that will be used for the sequence simulations.
minRate	Minimum rate value to test.
maxRate	Maximum rate value to test.

Returns: A method that can be evaluated to determine the scaling factor that, when applied to a sequence simulation done using the specified tree and rate matrix, will produce at the tips a sequence alignment with the specified (average) percent identity.

Definition at line 211 of file SequenceSimulation.public.cs.

◆ GetScale()

delegate double PhyloTree.SequenceSimulation.SequenceSimulation.GetScale ( double conservation )

Represents a function that can be evaluated to return the scaling factor to use in order to obtain the specified average conservation .

Parameters

conservation The average conservation whose corresponding scaling factor will be returned.

Returns: The scaling factor that will produce the speicfied average conservation .

◆ SimulateAllSequences() [1/2]

static Dictionary< string, Sequence > PhyloTree.SequenceSimulation.SequenceSimulation.SimulateAllSequences	(	this TreeNode	tree,
		int	ancestralSequenceLength,
		RateMatrix	rateMatrix,
		double	scale = `1`,
		IndelModel	indelModel = `null`
	)

static

Simulates the evolution of a random ancestral sequence with the specified length over a phylogenetic tree , with the specified rate matrix, scale factor, and insertion/deletion model.

Parameters

tree	The tree over which the sequence evolves. This is assumed to be rooted (i.e., the ancestral sequence is placed at the root of the tree).
ancestralSequenceLength	The length of the ancestral sequence whose evolution is being simulated. Note that if insertions/deletions are allowed to happen, the final length of the (aligned) sequences may differ from this.
rateMatrix	The rate matrix that governs the evolution of the sequence.
scale	A scaling factor. If this is different from 1, the effect is the same as multiplying the branch lengths of the tree or the rate matrix by the supplied value.
indelModel	The model for insertions/deletions. If this is null, no insertions/deletions are allowed to happen.

Returns: A Dictionary<String, Sequence> containing entries for all the nodes in the tree. For each entry, the key is a string containing the TreeNode.Id of the node, and the value is a Sequence containing the sequence. The sequences are all aligned.

Definition at line 187 of file SequenceSimulation.public.cs.

◆ SimulateAllSequences() [2/2]

static Dictionary< string, Sequence > PhyloTree.SequenceSimulation.SequenceSimulation.SimulateAllSequences	(	this TreeNode	tree,
		Sequence	ancestralSequence,
		RateMatrix	rateMatrix,
		double	scale = `1`,
		IndelModel	indelModel = `null`
	)

static

Simulates the evolution of the specified ancestral sequence over a phylogenetic tree , with the specified rate matrix, scale factor, and insertion/deletion model.

Parameters

tree	The tree over which the sequence evolves. This is assumed to be rooted (i.e., the ancestral sequence is placed at the root of the tree).
ancestralSequence	The ancestral sequence whose evolution is being simulated.
rateMatrix	The rate matrix that governs the evolution of the sequence.
scale	A scaling factor. If this is different from 1, the effect is the same as multiplying the branch lengths of the tree or the rate matrix by the supplied value.
indelModel	The model for insertions/deletions. If this is null, no insertions/deletions are allowed to happen.

Returns: A Dictionary<String, Sequence> containing entries for all the nodes in the tree. For each entry, the key is a string containing the TreeNode.Id of the node, and the value is a Sequence containing the sequence. The sequences are all aligned.

Definition at line 116 of file SequenceSimulation.public.cs.

◆ SimulateSequences() [1/2]

static Dictionary< string, Sequence > PhyloTree.SequenceSimulation.SequenceSimulation.SimulateSequences	(	this TreeNode	tree,
		int	ancestralSequenceLength,
		RateMatrix	rateMatrix,
		double	scale = `1`,
		IndelModel	indelModel = `null`
	)

static

Simulates the evolution of a random ancestral sequence with the specified length over a phylogenetic tree , with the specified rate matrix, scale factor, and insertion/deletion model.

Parameters

tree	The tree over which the sequence evolves. This is assumed to be rooted (i.e., the ancestral sequence is placed at the root of the tree).
ancestralSequenceLength	The length of the ancestral sequence whose evolution is being simulated. Note that if insertions/deletions are allowed to happen, the final length of the (aligned) sequences may differ from this.
rateMatrix	The rate matrix that governs the evolution of the sequence.
scale	A scaling factor. If this is different from 1, the effect is the same as multiplying the branch lengths of the tree or the rate matrix by the supplied value.
indelModel	The model for insertions/deletions. If this is null, no insertions/deletions are allowed to happen.

Returns: A Dictionary<String, Sequence> containing entries for all the nodes in the tree that have names. For each entry, the key is a string containing the TreeNode.Name of the node, and the value is a Sequence containing the sequence. The sequences are all aligned.

Definition at line 97 of file SequenceSimulation.public.cs.

◆ SimulateSequences() [2/2]

static Dictionary< string, Sequence > PhyloTree.SequenceSimulation.SequenceSimulation.SimulateSequences	(	this TreeNode	tree,
		Sequence	ancestralSequence,
		RateMatrix	rateMatrix,
		double	scale = `1`,
		IndelModel	indelModel = `null`
	)

static

Simulates the evolution of the specified ancestral sequence over a phylogenetic tree , with the specified rate matrix, scale factor, and insertion/deletion model.

Parameters

tree	The tree over which the sequence evolves. This is assumed to be rooted (i.e., the ancestral sequence is placed at the root of the tree).
ancestralSequence	The ancestral sequence whose evolution is being simulated.
rateMatrix	The rate matrix that governs the evolution of the sequence.
scale	A scaling factor. If this is different from 1, the effect is the same as multiplying the branch lengths of the tree or the rate matrix by the supplied value.
indelModel	The model for insertions/deletions. If this is null, no insertions/deletions are allowed to happen.

Returns: A Dictionary<String, Sequence> containing entries for all the nodes in the tree that have names. For each entry, the key is a string containing the TreeNode.Name of the node, and the value is a Sequence containing the sequence. The sequences are all aligned.

Definition at line 23 of file SequenceSimulation.public.cs.

◆ ToStringAlignment()

static Dictionary< string, string > PhyloTree.SequenceSimulation.SequenceSimulation.ToStringAlignment ( this Dictionary< string, Sequence > alignment )

static

Converts a sequence alignment where the sequences are stored as Sequences into an alignment where the sequences are stored as strings.

Parameters

alignment The alignment to convert.

Returns: A Dictionary<String, String> where both keys and values are string.

Definition at line 310 of file SequenceSimulation.public.cs.

Property Documentation

◆ RandomNumberGenerator

Random PhyloTree.SequenceSimulation.SequenceSimulation.RandomNumberGenerator = new ThreadSafeRandom()

staticgetset

The random number generator used to simulate sequence evolution. If you change this, please ensure that it is thread-safe.

Definition at line 21 of file SequenceSimulation.cs.

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

SequenceSimulation/SequenceSimulation.cs
SequenceSimulation/SequenceSimulation.public.cs

Public Member Functions

Static Public Member Functions

Properties

Detailed Description

Member Function Documentation

◆ ConservationToScale()

◆ GetScale()

◆ SimulateAllSequences() [1/2]

◆ SimulateAllSequences() [2/2]

◆ SimulateSequences() [1/2]

◆ SimulateSequences() [2/2]

◆ ToStringAlignment()

Property Documentation

◆ RandomNumberGenerator