The BioNJ distance method. More...

#include <Bpp/Phyl/Distance/BioNJ.h>

Inheritance diagram for bpp::BioNJ:

Collaboration diagram for bpp::BioNJ:

Public Member Functions
	BioNJ (bool rooted=false, bool positiveLengths=false, bool verbose=true)
	Create a new BioNJ object instance and compute a tree from a distance matrix. More...

	BioNJ (const DistanceMatrix &matrix, bool rooted=false, bool positiveLengths=false, bool verbose=true)
	Create a new BioNJ object instance and compute a tree from a distance matrix. More...

BioNJ *	clone () const

virtual	~BioNJ ()

std::string	getName () const

void	setDistanceMatrix (const DistanceMatrix &matrix)
	Set the distance matrix to use. More...

void	computeTree ()
	Compute the tree corresponding to the distance matrix. More...

double	computeDistancesFromPair (const std::vector< size_t > &pair, const std::vector< double > &branchLengths, size_t pos)
	Actualizes the distance matrix according to a given pair and the corresponding branch lengths. More...

virtual void	outputPositiveLengths (bool yn)

bool	hasTree () const override

const Tree &	tree () const override

void	setVerbose (bool yn) override

bool	isVerbose () const override

Protected Member Functions
std::vector< size_t >	getBestPair ()
	Get the best pair of nodes to agglomerate. More...

std::vector< double >	computeBranchLengthsForPair (const std::vector< size_t > &pair)
	Compute the branch lengths for two nodes to agglomerate. More...

void	finalStep (int idRoot)
	Method called when there ar eonly three remaining node to agglomerate, and creates the root node of the tree. More...

Specific methods.
virtual Node *	getLeafNode (int id, const std::string &name)
	Get a leaf node. More...

virtual Node *	getParentNode (int id, Node son1, Node son2)
	Get an inner node. More...

Protected Attributes
std::vector< double >	sumDist_

bool	positiveLengths_

DistanceMatrix	matrix_

std::unique_ptr< Tree >	tree_

std::map< size_t, Node * >	currentNodes_

bool	verbose_

bool	rootTree_

Private Attributes
DistanceMatrix	variance_

double	lambda_

Detailed Description

The BioNJ distance method.

Reference: Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol. 1997 Jul;14(7):685-95.

Definition at line 21 of file BioNJ.h.

Constructor & Destructor Documentation

◆ BioNJ() [1/2]

bpp::BioNJ::BioNJ	(	bool	rooted = `false`,
		bool	positiveLengths = `false`,
		bool	verbose = `true`
	)

inline

Create a new BioNJ object instance and compute a tree from a distance matrix.

Parameters

rooted	Tell if the output tree should be rooted.
positiveLengths	Tell if negative lengths should be avoided.
verbose	Allow to display extra information, like progress bars.

Definition at line 36 of file BioNJ.h.

Referenced by clone().

◆ BioNJ() [2/2]

bpp::BioNJ::BioNJ	(	const DistanceMatrix &	matrix,
		bool	rooted = `false`,
		bool	positiveLengths = `false`,
		bool	verbose = `true`
	)

inline

Create a new BioNJ object instance and compute a tree from a distance matrix.

Parameters

matrix	Input distance matrix.
rooted	Tell if the output tree should be rooted.
positiveLengths	Tell if negative lengths should be avoided.
verbose	Allow to display extra information, like progress bars.

Definition at line 49 of file BioNJ.h.

References computeTree(), bpp::NeighborJoining::outputPositiveLengths(), and setDistanceMatrix().

◆ ~BioNJ()

virtual bpp::BioNJ::~BioNJ ( )

inlinevirtual

Definition at line 62 of file BioNJ.h.

Member Function Documentation

◆ clone()

BioNJ* bpp::BioNJ::clone ( ) const

inlinevirtual

Implements bpp::AgglomerativeDistanceMethodInterface.

Definition at line 60 of file BioNJ.h.

References BioNJ().

◆ computeBranchLengthsForPair()

std::vector< double > NeighborJoining::computeBranchLengthsForPair ( const std::vector< size_t > & pair )

protectedvirtualinherited

Compute the branch lengths for two nodes to agglomerate.

+---l1-----N1
|
+---l2-----N2

This method compute l1 and l2 given N1 and N2.

Parameters

pair	The indices of the nodes to be agglomerated.

Returns: A size 2 vector with branch lengths.

Implements bpp::AbstractAgglomerativeDistanceMethod.

Definition at line 56 of file NeighborJoining.cpp.

◆ computeDistancesFromPair()

double BioNJ::computeDistancesFromPair	(	const std::vector< size_t > &	pair,
		const std::vector< double > &	branchLengths,
		size_t	pos
	)

virtual

Actualizes the distance matrix according to a given pair and the corresponding branch lengths.

Parameters

pair	The indices of the nodes to be agglomerated.
branchLengths	The corresponding branch lengths.
pos	The index of the node whose distance ust be updated.

Returns: The distance between the 'pos' node and the agglomerated pair.

Implements bpp::AbstractAgglomerativeDistanceMethod.

Definition at line 18 of file BioNJ.cpp.

◆ computeTree()

void BioNJ::computeTree ( )

virtual

Compute the tree corresponding to the distance matrix.

This method implements the following algorithm: 1) Build all leaf nodes (getLeafNode method) 2) Get the best pair to agglomerate (getBestPair method) 3) Compute the branch lengths for this pair (computeBranchLengthsForPair method) 4) Build the parent node of the pair (getParentNode method) 5) For each remaining node, update distances from the pair (computeDistancesFromPair method) 6) Return to step 2 while there are more than 3 remaining nodes. 7) Perform the final step, and send a rooted or unrooted tree.

Reimplemented from bpp::AbstractAgglomerativeDistanceMethod.

Definition at line 25 of file BioNJ.cpp.

References bpp::ApplicationTools::displayGauge(), and bpp::Node::setDistanceToFather().

Referenced by BioNJ().