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)

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.

Macro Definition Documentation

AVG

#define AVG	(		x,
			y )

Value:

(((x) + (y))/2)

TRACE

#define TRACE   0

Typedef Documentation

dist_t

typedef float dist_t

ulong

typedef unsigned long int ulong

Function Documentation

CalcDistRange()

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

MuscleUpgma2()

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

TriangleSubscript()

ulong TriangleSubscript	(	uint	uIndex1,
		uint	uIndex2 )