Contains methods to compute distance matrices. More...

Static Public Member Functions
static float[][]	BuildFromAlignment (IReadOnlyList< byte[]> sequences, EvolutionModel evolutionModel=EvolutionModel.Kimura, int numCores=-1, Action< double > progressCallback=null)
	Build a distance matrix from aligned DNA sequences stored as a T:byte[] array where each byte corresponds to three positions. More...

static float[][]	BuildFromAlignment (IReadOnlyList< ushort[]> sequences, EvolutionModel evolutionModel=EvolutionModel.Kimura, int numCores=-1, Action< double > progressCallback=null)
	Build a distance matrix from aligned protein sequences stored as a T:ushort[] array where each ushort corresponds to two positions. More...

static void	BuildFromAlignment (float[][] allocatedMatrix, IReadOnlyList< byte[]> sequences, EvolutionModel evolutionModel=EvolutionModel.Kimura, int numCores=-1, Action< double > progressCallback=null)
	Build a distance matrix from aligned DNA sequences stored as a T:byte[] array where each byte corresponds to three positions. More...

static void	BuildFromAlignment (float[][] allocatedMatrix, IReadOnlyList< ushort[]> sequences, EvolutionModel evolutionModel=EvolutionModel.Kimura, int numCores=0, Action< double > progressCallback=null)
	Build a distance matrix from aligned protein sequences stored as a T:ushort[] array where each ushort corresponds to two positions. More...

static void	BuildFromAlignment (float[][] allocatedMatrix, IReadOnlyList< string > sequences, AlignmentType alignmentType=AlignmentType.Autodetect, EvolutionModel evolutionModel=EvolutionModel.Kimura, int numCores=0, Action< double > progressCallback=null)
	Build a distance matrix from aligned DNA or protein sequences. More...

static float[][]	BuildFromAlignment (IReadOnlyList< string > sequences, AlignmentType alignmentType=AlignmentType.Autodetect, EvolutionModel evolutionModel=EvolutionModel.Kimura, int numCores=0, Action< double > progressCallback=null)
	Build a distance matrix from aligned DNA or protein sequences. More...

static void	BootstrapReplicateFromAlignment (float[][] allocatedMatrix, IReadOnlyList< string > sequences, AlignmentType alignmentType=AlignmentType.Autodetect, EvolutionModel evolutionModel=EvolutionModel.Kimura, int numCores=0, Action< double > progressCallback=null)
	Build a bootstrap replicate of a distance matrix from aligned DNA or protein sequences. More...

static float[][]	BootstrapReplicateFromAlignment (IReadOnlyList< string > sequences, AlignmentType alignmentType=AlignmentType.Autodetect, EvolutionModel evolutionModel=EvolutionModel.Kimura, int numCores=0, Action< double > progressCallback=null)
	Build a bootstrap replicate of a distance matrix from aligned DNA or protein sequences. More...

static float[][]	BuildFromAlignment (Dictionary< string, string > alignment, AlignmentType alignmentType=AlignmentType.Autodetect, EvolutionModel evolutionModel=EvolutionModel.Kimura, int numCores=0, Action< double > progressCallback=null)
	Build a distance matrix from aligned DNA or protein sequences. More...

static void	BuildFromAlignment (float[][] allocatedMatrix, Dictionary< string, string > alignment, AlignmentType alignmentType=AlignmentType.Autodetect, EvolutionModel evolutionModel=EvolutionModel.Kimura, int numCores=0, Action< double > progressCallback=null)
	Build a distance matrix from aligned DNA or protein sequences. More...

static float[][]	BootstrapReplicateFromAlignment (Dictionary< string, string > alignment, AlignmentType alignmentType=AlignmentType.Autodetect, EvolutionModel evolutionModel=EvolutionModel.Kimura, int numCores=0, Action< double > progressCallback=null)
	Build a bootstrap replicate of a distance matrix from aligned DNA or protein sequences. More...

static void	BootstrapReplicateFromAlignment (float[][] allocatedMatrix, Dictionary< string, string > alignment, AlignmentType alignmentType=AlignmentType.Autodetect, EvolutionModel evolutionModel=EvolutionModel.Kimura, int numCores=0, Action< double > progressCallback=null)
	Build a bootstrap replicate of a distance matrix from aligned DNA or protein sequences. More...

static IEnumerable< byte[]>	ConvertDNASequences (IEnumerable< string > sequences)
	Convert DNA sequences into T:byte[] arrays in which each byte corresponds to 3 positions. More...

static List< byte[]>	ConvertDNASequences (IReadOnlyList< string > sequences)
	Convert DNA sequences into T:byte[] arrays in which each byte corresponds to 3 positions. More...

static IEnumerable< byte[]>	BootstrapDNASequences (IEnumerable< string > sequences)
	Computes a bootstrap replicate of a DNA sequence alignment. More...

static List< byte[]>	BootstrapDNASequences (IReadOnlyList< string > sequences)
	Computes a bootstrap replicate of a DNA sequence alignment. More...

static IEnumerable< ushort[]>	ConvertProteinSequences (IEnumerable< string > sequences)
	Convert protein sequences into T:ushort[] arrays in which each ushort corresponds to 2 positions. More...

static List< ushort[]>	ConvertProteinSequences (IReadOnlyList< string > sequences)
	Convert protein sequences into T:ushort[] arrays in which each ushort corresponds to 2 positions. More...

static IEnumerable< ushort[]>	BootstrapProteinSequences (IEnumerable< string > sequences)
	Computes a bootstrap replicate of a protein sequence alignment. More...

static List< ushort[]>	BootstrapProteinSequences (IReadOnlyList< string > sequences)
	Computes a bootstrap replicate of a protein sequence alignment. More...

static ushort[]	ConvertProteinSequence (string sequence)
	Converts a protein sequence stored as a string into a T:ushort[] array. Each ushort contains 2 amino acid positions. The allowed symbols are the usual 20 1-letter amino acid abbreviations, plus U for Sec, O for Pyl, B for Asn or Asp, Z for Gln or Glu, J for Ile or Leu, X for any amino acid, * for stop codons and - for gaps (uppercase and lowercase). All other characters are treated as gaps. If the sequence length is not a multiple of 2, it is padded with gaps. More...

static float	CompareProteinSequencesBLOSUM62 (ushort[] sequence1, ushort[] sequence2, int selfScore1, int selfScore2)
	Compares two protein sequences using the Scoredist correction with the BLOSUM62 matrix. More...

Detailed Description

Contains methods to compute distance matrices.

Definition at line 66 of file DistanceMatrix.cs.

Member Function Documentation

◆ BootstrapDNASequences() [1/2]

static IEnumerable< byte[]> PhyloTree.TreeBuilding.DistanceMatrix.BootstrapDNASequences ( IEnumerable< string > sequences )

static

Computes a bootstrap replicate of a DNA sequence alignment.

Parameters

sequences The aligned DNA sequences.

Returns: An T:IEnumerable<byte[]> that, when enumerated, will contain the bootstrapped sequences, converted into T:byte[] arrays where each byte corresponds to 3 positions.

Exceptions

ArgumentOutOfRangeException Thrown if not all of the sequences have the same length.

Definition at line 533 of file DistanceMatrix.cs.

◆ BootstrapDNASequences() [2/2]

static List< byte[]> PhyloTree.TreeBuilding.DistanceMatrix.BootstrapDNASequences ( IReadOnlyList< string > sequences )

static

Computes a bootstrap replicate of a DNA sequence alignment.

Parameters

sequences The aligned DNA sequences.

Returns: An T:List<byte[]> that contains the bootstrapped sequences, converted into T:byte[] arrays where each byte corresponds to 3 positions.

Exceptions

ArgumentOutOfRangeException Thrown if not all of the sequences have the same length.

Definition at line 562 of file DistanceMatrix.cs.

◆ BootstrapProteinSequences() [1/2]

static IEnumerable< ushort[]> PhyloTree.TreeBuilding.DistanceMatrix.BootstrapProteinSequences ( IEnumerable< string > sequences )

static

Computes a bootstrap replicate of a protein sequence alignment.

Parameters

sequences The aligned protein sequences.

Returns: An T:IEnumerable<ushort[]> that, when enumerated, will contain the bootstrapped sequences, converted into T:ushort[] arrays where each ushort corresponds to 2 positions.

Exceptions

ArgumentOutOfRangeException Thrown if not all of the sequences have the same length.

Definition at line 596 of file DistanceMatrix.cs.

◆ BootstrapProteinSequences() [2/2]

static List< ushort[]> PhyloTree.TreeBuilding.DistanceMatrix.BootstrapProteinSequences ( IReadOnlyList< string > sequences )

static

Computes a bootstrap replicate of a protein sequence alignment.

Parameters

sequences The aligned protein sequences.

Returns: A T:List<ushort[]> that contains the bootstrapped sequences, converted into T:ushort[] arrays where each ushort corresponds to 2 positions.

Exceptions

ArgumentOutOfRangeException Thrown if not all of the sequences have the same length.

Definition at line 625 of file DistanceMatrix.cs.

◆ BootstrapReplicateFromAlignment() [1/4]

static float[][] PhyloTree.TreeBuilding.DistanceMatrix.BootstrapReplicateFromAlignment	(	Dictionary< string, string >	alignment,
		AlignmentType	alignmentType = `AlignmentType.Autodetect`,
		EvolutionModel	evolutionModel = `EvolutionModel.Kimura`,
		int	numCores = `0`,
		Action< double >	progressCallback = `null`
	)

static

Build a bootstrap replicate of a distance matrix from aligned DNA or protein sequences.

Parameters

alignment	The aligned sequences. These will be resampled randomly.
alignmentType	The type of sequences in the alignment.
evolutionModel	The evolutionary model to use to compute the distance matrix.
numCores	The maximum number of threads to use, or -1 to let the runtime decide.
progressCallback	A method used to report progress.

Returns: A T:float[][] jagged array containing the lower-triangular distance matrix.

Definition at line 462 of file DistanceMatrix.cs.

◆ BootstrapReplicateFromAlignment() [2/4]

static void PhyloTree.TreeBuilding.DistanceMatrix.BootstrapReplicateFromAlignment	(	float	allocatedMatrix[][],
		Dictionary< string, string >	alignment,
		AlignmentType	alignmentType = `AlignmentType.Autodetect`,
		EvolutionModel	evolutionModel = `EvolutionModel.Kimura`,
		int	numCores = `0`,
		Action< double >	progressCallback = `null`
	)

static

Build a bootstrap replicate of a distance matrix from aligned DNA or protein sequences.

Parameters

allocatedMatrix	A pre-allocated T:float[][] jagged array that will contain the lower-triangular distance matrix.
alignment	The aligned sequences. These will be resampled randomly.
alignmentType	The type of sequences in the alignment.
evolutionModel	The evolutionary model to use to compute the distance matrix.
numCores	The maximum number of threads to use, or -1 to let the runtime decide.
progressCallback	A method used to report progress.

Definition at line 476 of file DistanceMatrix.cs.

◆ BootstrapReplicateFromAlignment() [3/4]

static void PhyloTree.TreeBuilding.DistanceMatrix.BootstrapReplicateFromAlignment	(	float	allocatedMatrix[][],
		IReadOnlyList< string >	sequences,
		AlignmentType	alignmentType = `AlignmentType.Autodetect`,
		EvolutionModel	evolutionModel = `EvolutionModel.Kimura`,
		int	numCores = `0`,
		Action< double >	progressCallback = `null`
	)

static

Build a bootstrap replicate of a distance matrix from aligned DNA or protein sequences.

Parameters

allocatedMatrix	A pre-allocated T:float[][] jagged array that will contain the lower-triangular distance matrix.
sequences	The aligned sequences. These will be resampled randomly.
alignmentType	The type of sequences in the alignment.
evolutionModel	The evolutionary model to use to compute the distance matrix.
numCores	The maximum number of threads to use, or -1 to let the runtime decide.
progressCallback	A method used to report progress.

Definition at line 355 of file DistanceMatrix.cs.

◆ BootstrapReplicateFromAlignment() [4/4]

static float[][] PhyloTree.TreeBuilding.DistanceMatrix.BootstrapReplicateFromAlignment	(	IReadOnlyList< string >	sequences,
		AlignmentType	alignmentType = `AlignmentType.Autodetect`,
		EvolutionModel	evolutionModel = `EvolutionModel.Kimura`,
		int	numCores = `0`,
		Action< double >	progressCallback = `null`
	)

static

Build a bootstrap replicate of a distance matrix from aligned DNA or protein sequences.

Parameters

sequences	The aligned sequences. These will be resampled randomly.
alignmentType	The type of sequences in the alignment.
evolutionModel	The evolutionary model to use to compute the distance matrix.
numCores	The maximum number of threads to use, or -1 to let the runtime decide.
progressCallback	A method used to report progress.

Returns: A T:float[][] jagged array containing the lower-triangular distance matrix.

Definition at line 411 of file DistanceMatrix.cs.

◆ BuildFromAlignment() [1/8]

static float[][] PhyloTree.TreeBuilding.DistanceMatrix.BuildFromAlignment	(	Dictionary< string, string >	alignment,
		AlignmentType	alignmentType = `AlignmentType.Autodetect`,
		EvolutionModel	evolutionModel = `EvolutionModel.Kimura`,
		int	numCores = `0`,
		Action< double >	progressCallback = `null`
	)

static

Build a distance matrix from aligned DNA or protein sequences.

Parameters

alignment	The aligned sequences.
alignmentType	The type of sequences in the alignment.
evolutionModel	The evolutionary model to use to compute the distance matrix.
numCores	The maximum number of threads to use, or -1 to let the runtime decide.
progressCallback	A method used to report progress.

Returns: A T:float[][] jagged array containing the lower-triangular distance matrix.

Definition at line 434 of file DistanceMatrix.cs.

◆ BuildFromAlignment() [2/8]

static void PhyloTree.TreeBuilding.DistanceMatrix.BuildFromAlignment	(	float	allocatedMatrix[][],
		Dictionary< string, string >	alignment,
		AlignmentType	alignmentType = `AlignmentType.Autodetect`,
		EvolutionModel	evolutionModel = `EvolutionModel.Kimura`,
		int	numCores = `0`,
		Action< double >	progressCallback = `null`
	)

static

Build a distance matrix from aligned DNA or protein sequences.

Parameters

allocatedMatrix	A pre-allocated T:float[][] jagged array that will contain the lower-triangular distance matrix.
alignment	The aligned sequences.
alignmentType	The type of sequences in the alignment.
evolutionModel	The evolutionary model to use to compute the distance matrix.
numCores	The maximum number of threads to use, or -1 to let the runtime decide.
progressCallback	A method used to report progress.

Definition at line 448 of file DistanceMatrix.cs.

◆ BuildFromAlignment() [3/8]

static void PhyloTree.TreeBuilding.DistanceMatrix.BuildFromAlignment	(	float	allocatedMatrix[][],
		IReadOnlyList< byte[]>	sequences,
		EvolutionModel	evolutionModel = `EvolutionModel.Kimura`,
		int	numCores = `-1`,
		Action< double >	progressCallback = `null`
	)

static

Build a distance matrix from aligned DNA sequences stored as a T:byte[] array where each byte corresponds to three positions.

Parameters

allocatedMatrix	A pre-allocated T:float[][] jagged array that will contain the lower-triangular distance matrix.
sequences	The aligned sequences.
evolutionModel	The evolutionary model to use to compute the distance matrix.
numCores	The maximum number of threads to use, or -1 to let the runtime decide.
progressCallback	A method used to report progress.

Definition at line 171 of file DistanceMatrix.cs.

◆ BuildFromAlignment() [4/8]

static void PhyloTree.TreeBuilding.DistanceMatrix.BuildFromAlignment	(	float	allocatedMatrix[][],
		IReadOnlyList< string >	sequences,
		AlignmentType	alignmentType = `AlignmentType.Autodetect`,
		EvolutionModel	evolutionModel = `EvolutionModel.Kimura`,
		int	numCores = `0`,
		Action< double >	progressCallback = `null`
	)

static

Build a distance matrix from aligned DNA or protein sequences.

Parameters

allocatedMatrix	A pre-allocated T:float[][] jagged array that will contain the lower-triangular distance matrix.
sequences	The aligned sequences.
alignmentType	The type of sequences in the alignment.
evolutionModel	The evolutionary model to use to compute the distance matrix.
numCores	The maximum number of threads to use, or -1 to let the runtime decide.
progressCallback	A method used to report progress.

Definition at line 252 of file DistanceMatrix.cs.

◆ BuildFromAlignment() [5/8]

static void PhyloTree.TreeBuilding.DistanceMatrix.BuildFromAlignment	(	float	allocatedMatrix[][],
		IReadOnlyList< ushort[]>	sequences,
		EvolutionModel	evolutionModel = `EvolutionModel.Kimura`,
		int	numCores = `0`,
		Action< double >	progressCallback = `null`
	)

static

Build a distance matrix from aligned protein sequences stored as a T:ushort[] array where each ushort corresponds to two positions.

Parameters

allocatedMatrix	A pre-allocated T:float[][] jagged array that will contain the lower-triangular distance matrix.
sequences	The aligned sequences.
evolutionModel	The evolutionary model to use to compute the distance matrix.
numCores	The maximum number of threads to use, or -1 to let the runtime decide.
progressCallback	A method used to report progress.

Definition at line 211 of file DistanceMatrix.cs.

◆ BuildFromAlignment() [6/8]

static float[][] PhyloTree.TreeBuilding.DistanceMatrix.BuildFromAlignment	(	IReadOnlyList< byte[]>	sequences,
		EvolutionModel	evolutionModel = `EvolutionModel.Kimura`,
		int	numCores = `-1`,
		Action< double >	progressCallback = `null`
	)

static

Build a distance matrix from aligned DNA sequences stored as a T:byte[] array where each byte corresponds to three positions.

Parameters

sequences	The aligned sequences.
evolutionModel	The evolutionary model to use to compute the distance matrix.
numCores	The maximum number of threads to use, or -1 to let the runtime decide.
progressCallback	A method used to report progress.

Returns: A T:float[][] jagged array containing the lower-triangular distance matrix.

Definition at line 127 of file DistanceMatrix.cs.

◆ BuildFromAlignment() [7/8]

static float[][] PhyloTree.TreeBuilding.DistanceMatrix.BuildFromAlignment	(	IReadOnlyList< string >	sequences,
		AlignmentType	alignmentType = `AlignmentType.Autodetect`,
		EvolutionModel	evolutionModel = `EvolutionModel.Kimura`,
		int	numCores = `0`,
		Action< double >	progressCallback = `null`
	)

static

Build a distance matrix from aligned DNA or protein sequences.

Parameters

sequences	The aligned sequences.
alignmentType	The type of sequences in the alignment.
evolutionModel	The evolutionary model to use to compute the distance matrix.
numCores	The maximum number of threads to use, or -1 to let the runtime decide.
progressCallback	A method used to report progress.

Returns: A T:float[][] jagged array containing the lower-triangular distance matrix.

Definition at line 332 of file DistanceMatrix.cs.

◆ BuildFromAlignment() [8/8]

static float[][] PhyloTree.TreeBuilding.DistanceMatrix.BuildFromAlignment	(	IReadOnlyList< ushort[]>	sequences,
		EvolutionModel	evolutionModel = `EvolutionModel.Kimura`,
		int	numCores = `-1`,
		Action< double >	progressCallback = `null`
	)

static

Build a distance matrix from aligned protein sequences stored as a T:ushort[] array where each ushort corresponds to two positions.

Parameters

sequences	The aligned sequences.
evolutionModel	The evolutionary model to use to compute the distance matrix.
numCores	The maximum number of threads to use, or -1 to let the runtime decide.
progressCallback	A method used to report progress.

Returns: A T:float[][] jagged array containing the lower-triangular distance matrix.

Definition at line 149 of file DistanceMatrix.cs.

◆ CompareProteinSequencesBLOSUM62()

static float PhyloTree.TreeBuilding.DistanceMatrix.CompareProteinSequencesBLOSUM62	(	ushort[]	sequence1,
		ushort[]	sequence2,
		int	selfScore1,
		int	selfScore2
	)

static

Compares two protein sequences using the Scoredist correction with the BLOSUM62 matrix.

Parameters

sequence1	The first sequence.
sequence2	The second sequence.
selfScore1	The score obtained by comparing sequence1 with itself.
selfScore2	The score obtained by comparing sequence2 with itself.

Returns: The distance between the two sequences.

Definition at line 779 of file DistanceMatrix.Protein.cs.

◆ ConvertDNASequences() [1/2]

static IEnumerable< byte[]> PhyloTree.TreeBuilding.DistanceMatrix.ConvertDNASequences ( IEnumerable< string > sequences )

static

Convert DNA sequences into T:byte[] arrays in which each byte corresponds to 3 positions.

Parameters

sequences The sequences to convert.

Returns: An T:IEnumerable<byte[]> that, when enumerated, will contain the converted sequences.

Definition at line 486 of file DistanceMatrix.cs.

◆ ConvertDNASequences() [2/2]

static List< byte[]> PhyloTree.TreeBuilding.DistanceMatrix.ConvertDNASequences ( IReadOnlyList< string > sequences )

static

Convert DNA sequences into T:byte[] arrays in which each byte corresponds to 3 positions.

Parameters

sequences The sequences to convert.

Returns: A T:List<byte[]> that contains the converted sequences.

Definition at line 499 of file DistanceMatrix.cs.

◆ ConvertProteinSequence()

static ushort[] PhyloTree.TreeBuilding.DistanceMatrix.ConvertProteinSequence ( string sequence )

static

Converts a protein sequence stored as a string into a T:ushort[] array. Each ushort contains 2 amino acid positions. The allowed symbols are the usual 20 1-letter amino acid abbreviations, plus U for Sec, O for Pyl, B for Asn or Asp, Z for Gln or Glu, J for Ile or Leu, X for any amino acid, * for stop codons and - for gaps (uppercase and lowercase). All other characters are treated as gaps. If the sequence length is not a multiple of 2, it is padded with gaps.

Parameters

sequence The sequence to convert.

Returns: A T:ushort[] array representing the sequence.

Definition at line 53 of file DistanceMatrix.Protein.cs.

◆ ConvertProteinSequences() [1/2]

static IEnumerable< ushort[]> PhyloTree.TreeBuilding.DistanceMatrix.ConvertProteinSequences ( IEnumerable< string > sequences )

static

Convert protein sequences into T:ushort[] arrays in which each ushort corresponds to 2 positions.

Parameters

sequences The sequences to convert.

Returns: An T:IEnumerable<ushort[]> that, when enumerated, will contain the converted sequences.

Definition at line 572 of file DistanceMatrix.cs.

◆ ConvertProteinSequences() [2/2]

static List< ushort[]> PhyloTree.TreeBuilding.DistanceMatrix.ConvertProteinSequences ( IReadOnlyList< string > sequences )

static

Convert protein sequences into T:ushort[] arrays in which each ushort corresponds to 2 positions.

Parameters

sequences The sequences to convert.

Returns: A T:List<ushort[]> that contains the converted sequences.

Definition at line 585 of file DistanceMatrix.cs.

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

TreeBuilding/DistanceMatrix.cs
TreeBuilding/DistanceMatrix.Protein.cs
TreeBuilding/DistanceMatrix.DNA.cs

Static Public Member Functions

Detailed Description

Member Function Documentation

◆ BootstrapDNASequences() [1/2]

◆ BootstrapDNASequences() [2/2]

◆ BootstrapProteinSequences() [1/2]

◆ BootstrapProteinSequences() [2/2]

◆ BootstrapReplicateFromAlignment() [1/4]

◆ BootstrapReplicateFromAlignment() [2/4]

◆ BootstrapReplicateFromAlignment() [3/4]

◆ BootstrapReplicateFromAlignment() [4/4]

◆ BuildFromAlignment() [1/8]

◆ BuildFromAlignment() [2/8]

◆ BuildFromAlignment() [3/8]

◆ BuildFromAlignment() [4/8]

◆ BuildFromAlignment() [5/8]

◆ BuildFromAlignment() [6/8]

◆ BuildFromAlignment() [7/8]

◆ BuildFromAlignment() [8/8]

◆ CompareProteinSequencesBLOSUM62()

◆ ConvertDNASequences() [1/2]

◆ ConvertDNASequences() [2/2]

◆ ConvertProteinSequence()

◆ ConvertProteinSequences() [1/2]

◆ ConvertProteinSequences() [2/2]