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:

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Defines
#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)
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.

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Define Documentation

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

#define MAX	(	x,
		y		)	((x) > (y) ? (x) : (y))

#define MIN	(	x,
		y		)	((x) < (y) ? (x) : (y))

#define TRACE   0

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Typedef Documentation

typedef float dist_t

typedef unsigned long int ulong

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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]	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

ulong TriangleSubscript	(	uint	uIndex1,
		uint	uIndex2
	)