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 ().
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.

Enumeration Type Documentation

anonymous enum

anonymous enum

Enumerator
LEFT_NODE
RGHT_NODE
PRNT_NODE
DIFF_NODE

Function Documentation

GuideTreeFromFile()

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

extern

Parameters

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

Returns

non-zero on error

GuideTreeUpgma()

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

extern

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()

TraverseTree()

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

extern

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