tree.h File Reference

#include "symmatrix.h"
#include "muscle_tree.h"
#include "seq.h"

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Enumerations
enum	{ LEFT_NODE = 0, RGHT_NODE, PRNT_NODE, DIFF_NODE }

Functions
void	GuideTreeUpgma (tree_t **tree, char **labels, symmatrix_t *tmat, char *ftree)
	Creates a UPGMA guide tree. This is a frontend function to the ported Muscle UPGMA code (). More...
int	GuideTreeFromFile (tree_t **tree, mseq_t *mseq, char *ftree)
void	TraverseTree (int **piOrderLR_p, tree_t *tree, mseq_t *mseq)
	Depth first traversal of tree, i.e. leaf nodes (sequences) will be visited first. Order can be used to guide progressive alignment order. More...

Enumeration Type Documentation

anonymous enum

Enumerator
LEFT_NODE
RGHT_NODE
PRNT_NODE
DIFF_NODE

Function Documentation

int GuideTreeFromFile	(	tree_t **	tree,
		mseq_t *	mseq,
		char *	ftree
	)

Parameters

[out]	tree	created upgma tree. will be allocated here. use FreeMuscleTree() to free
[in]	mseq
[in]	ftree

Returns

non-zero on error

void GuideTreeUpgma	(	tree_t **	tree,
		char **	labels,
		symmatrix_t *	distmat,
		char *	ftree
	)

Creates a UPGMA guide tree. This is a frontend function to the ported Muscle UPGMA code ().

Parameters

[out]	tree	created upgma tree. will be allocated here. use FreeMuscleTree() to free
[in]	labels	pointer to nseq sequence names
[in]	distmat	distance matrix
[in]	ftree	optional: if non-NULL, tree will be written to this files

See also

FreeMuscleTree()

MuscleUpgma2()

void TraverseTree	(	int **	piOrderLR_p,
		tree_t *	tree,
		mseq_t *	mseq
	)

Depth first traversal of tree, i.e. leaf nodes (sequences) will be visited first. Order can be used to guide progressive alignment order.

Parameters

[out]	piOrderLR_p	order in which left/right nodes (profiles) are to be aligned. allocated here; caller must free.
[in]	tree	The tree to traverse; has to be rooted
[in]	mseq	corresponding multiple sequence structure