Clustal Omega  1.1.0
Typedefs | Enumerations | Functions
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.

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]treenewly created rooted UPGMA tree
[in]distmatdistance matrix to be clustered
[in]linkagelinkage type
[in]namesleaf 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