src/clustal/muscle_upgma.h File Reference

#include "symmatrix.h"
#include "muscle_tree.h"

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Typedefs
typedef enum linkage_e	linkage_t
Enumerations
enum	linkage_e {   LINKAGE_MIN, LINKAGE_AVG, LINKAGE_MAX, LINKAGE_NEIGHBORJOINING,   LINKAGE_BIASED }
Functions
void	MuscleUpgma2 (tree_t *tree, symmatrix_t *distmat, linkage_t linkage, char **names)
	Creates a UPGMA in O(N^2) tree from given distmat.

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Typedef Documentation

typedef enum linkage_e linkage_t

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Enumeration Type Documentation

enum linkage_e

Enumerator:

LINKAGE_MIN
LINKAGE_AVG
LINKAGE_MAX
LINKAGE_NEIGHBORJOINING
LINKAGE_BIASED

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Function Documentation

void MuscleUpgma2	(	tree_t *	tree,
		symmatrix_t *	distmat,
		linkage_t	linkage,
		char **	names
	)

Creates a UPGMA in O(N^2) tree from given distmat.

Parameters:

[out]	tree	newly created rooted UPGMA tree
[in]	distmat	distance matrix to be clustered
[in]	linkage	linkage type
[in]	names	leaf names, will be copied

Note:

called UPGMA2() in Muscle3.7. caller has to free with FreeMuscleTree()

See also:

FreeMuscleTree()

left and right node indices, as well as left and right branch-length and height for for internal nodes