#include "symmatrix.h"
#include "muscle_tree.h"
#include "seq.h"
Go to the source code of this file.
|
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.
|
|
◆ anonymous enum
Enumerator |
---|
LEFT_NODE | |
RGHT_NODE | |
PRNT_NODE | |
DIFF_NODE | |
◆ 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 |