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. More...

Typedef Documentation

typedef enum linkage_e linkage_t

Enumeration Type Documentation

enum linkage_e

Enumerator
LINKAGE_MIN
LINKAGE_AVG
LINKAGE_MAX
LINKAGE_NEIGHBORJOINING
LINKAGE_BIASED

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