PhyloTree.TreeBuilding.NeighborJoining Class Reference

Contains methods to compute neighbour-joining trees. More...

Static Public Member Functions
static TreeNode	BuildTree (Dictionary< string, string > alignment, EvolutionModel evolutionModel=EvolutionModel.Kimura, int bootstrapReplicates=0, AlignmentType alignmentType=AlignmentType.Autodetect, TreeNode constraint=null, bool allowNegativeBranches=true, int numCores=-1, Action< double > progressCallback=null)
	Builds a neighbour-joining tree using data from a sequence alignment. This method first computes a distance matrix from the sequence alignment, and then uses the distance matrix to compute the tree. More...
static TreeNode	BuildTree (float[][] distanceMatrix, IReadOnlyList< string > sequenceNames, TreeNode constraint=null, bool copyMatrix=true, bool allowNegativeBranches=true, int numCores=-1, Action< double > progressCallback=null)
	Builds a neighbour-joining tree using data from a distance matrix. More...

Detailed Description

Contains methods to compute neighbour-joining trees.

Definition at line 13 of file NeighborJoining.cs.

Member Function Documentation

BuildTree() [1/2]

static TreeNode PhyloTree.TreeBuilding.NeighborJoining.BuildTree ( Dictionary< string, string >  alignment, EvolutionModel  evolutionModel = EvolutionModel.Kimura, int  bootstrapReplicates = 0, AlignmentType  alignmentType = AlignmentType.Autodetect, TreeNode  constraint = null, bool  allowNegativeBranches = true, int  numCores = -1, Action< double >  progressCallback = null  )

static

Builds a neighbour-joining tree using data from a sequence alignment. This method first computes a distance matrix from the sequence alignment, and then uses the distance matrix to compute the tree.

Parameters

alignment	The sequence alignment.
evolutionModel	The evolutionary model to use when computing the distance matrix.
bootstrapReplicates	The number of bootstrap replicates to perform.
alignmentType	The type of sequence alignment (DNA, protein, or autodetect).
constraint	An optional tree to constrain the search. The tree produced by this method will be compatible with this tree. The constraint tree can be multifurcating.
allowNegativeBranches	If this is true negative branches produced by the neighbour-joining algorithm are left untouched; otherwise, their (absolute) length is added to the sibling branch, and the negative length is set to 0.
numCores	Maximum number of threads to use, or -1 to let the runtime decide.
progressCallback	A method used to report progress.

Returns

The neighbour-joining tree built from the supplied alignment .

Definition at line 28 of file NeighborJoining.cs.

BuildTree() [2/2]

static TreeNode PhyloTree.TreeBuilding.NeighborJoining.BuildTree ( float  distanceMatrix[][], IReadOnlyList< string >  sequenceNames, TreeNode  constraint = null, bool  copyMatrix = true, bool  allowNegativeBranches = true, int  numCores = -1, Action< double >  progressCallback = null  )

static

Builds a neighbour-joining tree using data from a distance matrix.

Parameters

distanceMatrix	The distance matrix containg distances between the taxa. This can be a lower triangular matrix or a full matrix; values above the diagonal will not be used.
sequenceNames	The names of the taxa. The indices of this list should correspond to the rows and columns of the distanceMatrix .
constraint	An optional tree to constrain the search. The tree produced by this method will be compatible with this tree. The constraint tree can be multifurcating.
copyMatrix	If this is true, the matrix is copied before using it to compute the tree. If this is false, the matrix is not copied. Copying the matrix increases the memory used by the method, but note that if the matrix is not copied, it will be modified in-place!
allowNegativeBranches	If this is true negative branches produced by the neighbour-joining algorithm are left untouched; otherwise, their (absolute) length is added to the sibling branch, and the negative length is set to 0.
numCores	Maximum number of threads to use, or -1 to let the runtime decide.
progressCallback	A method used to report progress.

Returns

The neighbour-joining tree built from the supplied distanceMatrix .

Definition at line 131 of file NeighborJoining.cs.

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

• TreeBuilding/NeighborJoining.cs