#include "symmatrix.h"
#include "muscle_tree.h"
#include "seq.h"
Go to the source code of this file.
◆ anonymous enum
Enumerator |
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LEFT_NODE | |
RGHT_NODE | |
PRNT_NODE | |
DIFF_NODE | |
◆ GuideTreeFromFile()
int GuideTreeFromFile |
( |
tree_t ** |
tree, |
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mseq_t * |
mseq, |
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char * |
ftree |
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) |
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- 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, |
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char ** |
labels, |
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symmatrix_t * |
distmat, |
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char * |
ftree |
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) |
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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, |
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tree_t * |
tree, |
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mseq_t * |
mseq |
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) |
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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 |