Clustal Omega  1.2.1
Macros | Typedefs | Functions
muscle_upgma.c File Reference
#include <stdlib.h>
#include <stdio.h>
#include <assert.h>
#include "util.h"
#include "log.h"
#include "symmatrix.h"
#include "muscle_tree.h"
#include "muscle_upgma.h"
Include dependency graph for muscle_upgma.c:

Macros

#define TRACE   0
 
#define AVG(x, y)   (((x) + (y))/2)
 

Typedefs

typedef unsigned long int ulong
 
typedef float dist_t
 

Functions

ulong TriangleSubscript (uint uIndex1, uint uIndex2)
 
void CalcDistRange (symmatrix_t *distmat, uint i, dist_t *row)
 
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...
 

Macro Definition Documentation

#define AVG (   x,
 
)    (((x) + (y))/2)
#define TRACE   0

Typedef Documentation

typedef float dist_t
typedef unsigned long int ulong

Function Documentation

void CalcDistRange ( symmatrix_t distmat,
uint  i,
dist_t row 
)
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

ulong TriangleSubscript ( uint  uIndex1,
uint  uIndex2 
)