Clustal Omega  1.2.2
Functions
tree.c File Reference
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include "util.h"
#include "log.h"
#include "muscle_upgma.h"
#include "tree.h"
Include dependency graph for tree.c:

Functions

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 (). 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...
 

Function Documentation

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
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()
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