src/clustal/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:
This graph shows which files directly or indirectly include this file:


#define TRACE   0
#define MIN(x, y)   ((x) < (y) ? (x) : (y))
#define MAX(x, y)   ((x) > (y) ? (x) : (y))
#define AVG(x, y)   (((x) + (y))/2)


typedef unsigned long int ulong
typedef float dist_t


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.

Define Documentation

#define AVG ( x,
 )     (((x) + (y))/2)
#define MAX ( x,
 )     ((x) > (y) ? (x) : (y))
#define MIN ( x,
 )     ((x) < (y) ? (x) : (y))
#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.

[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
called UPGMA2() in Muscle3.7. caller has to free with FreeMuscleTree()
See also:

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 
Generated on Fri Aug 31 05:32:52 2012 for Clustal Omega by  doxygen 1.6.3