1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
|
/* RogueNaRok is an algorithm for the identification of rogue taxa in a set of phylogenetic trees.
*
* Moreover, the program collection comes with efficient implementations of
* * the unrooted leaf stability by Thorley and Wilkinson
* * the taxonomic instability index by Maddinson and Maddison
* * a maximum agreement subtree implementation (MAST) for unrooted trees
* * a tool for pruning taxa from a tree collection.
*
* Copyright October 2011 by Andre J. Aberer
*
* Tree I/O and parallel framework are derived from RAxML by Alexandros Stamatakis.
*
* This program is free software; you may redistribute it and/or
* modify its under the terms of the GNU General Public License as
* published by the Free Software Foundation; either version 2 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* General Public License for more details.
*
* For any other inquiries send an Email to Andre J. Aberer
* andre.aberer at googlemail.com
*
* When publishing work that is based on the results from RogueNaRok, please cite:
* Andre J. Aberer, Denis Krompaß, Alexandros Stamatakis. RogueNaRok: an Efficient and Exact Algorithm for Rogue Taxon Identification. (unpublished) 2011.
*
*/
#ifndef TREES_H
#define TREES_H
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include <assert.h>
#include "common.h"
#include "legacy.h"
extern unsigned int *mask32;
boolean isTip(int number, int maxTips);
char *writeTreeToString(All *tr, boolean printBranchLengths);
void readTree(char *fileName);
boolean setupTree (All *tr, char *bootstrapTrees);
void readBestTree(All *tr, FILE *file);
void readBootstrapTree(All *tr, FILE *file);
void hookupDefault (nodeptr p, nodeptr q, int numBranches);
nodeptr findAnyTip(nodeptr p, int numsp);
int treeFindTipByLabelString(char *str, All *tr);
int getTreeStringLength(char *fileName);
FILE *getNumberOfTrees(All *tr, char *fileName);
void freeTree(All *tr);
#endif
|
