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