Clustal Omega  1.2.4
Enumerations | Functions
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

anonymous enum
Enumerator
LEFT_NODE 
RGHT_NODE 
PRNT_NODE 
DIFF_NODE 

Function Documentation

◆ GuideTreeFromFile()

int GuideTreeFromFile ( tree_t **  tree,
mseq_t mseq,
char *  ftree 
)
Parameters
[out]treecreated 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 
)

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

Parameters
[out]treecreated upgma tree. will be allocated here. use FreeMuscleTree() to free
[in]labelspointer to nseq sequence names
[in]distmatdistance matrix
[in]ftreeoptional: 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 
)

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_porder in which left/right nodes (profiles) are to be aligned. allocated here; caller must free.
[in]treeThe tree to traverse; has to be rooted
[in]mseqcorresponding multiple sequence structure