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treeIO.c
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treeIO.c
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/* RAxML-VI-HPC (version 2.2) a program for sequential and parallel estimation of phylogenetic trees
* Copyright August 2006 by Alexandros Stamatakis
*
* Partially derived from
* fastDNAml, a program for estimation of phylogenetic trees from sequences by Gary J. Olsen
*
* and
*
* Programs of the PHYLIP package by Joe Felsenstein.
*
* 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 enquiries send an Email to Alexandros Stamatakis
* Alexandros.Stamatakis@epfl.ch
*
* When publishing work that is based on the results from RAxML-VI-HPC please cite:
*
* Alexandros Stamatakis:"RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models".
* Bioinformatics 2006; doi: 10.1093/bioinformatics/btl446
*/
#ifndef WIN32
#include <sys/times.h>
#include <sys/types.h>
#include <sys/time.h>
#include <unistd.h>
#endif
#include <math.h>
#include <time.h>
#include <stdlib.h>
#include <stdio.h>
#include <ctype.h>
#include <string.h>
#include "axml.h"
extern FILE *INFILE;
extern char infoFileName[1024];
extern char tree_file[1024];
extern char *likelihood_key;
extern char *ntaxa_key;
extern char *smoothed_key;
extern int partCount;
extern double masterTime;
stringHashtable *initStringHashTable(hashNumberType n)
{
/*
init with primes
*/
static const hashNumberType initTable[] = {53, 97, 193, 389, 769, 1543, 3079, 6151, 12289, 24593, 49157, 98317,
196613, 393241, 786433, 1572869, 3145739, 6291469, 12582917, 25165843,
50331653, 100663319, 201326611, 402653189, 805306457, 1610612741};
/* init with powers of two
static const hashNumberType initTable[] = {64, 128, 256, 512, 1024, 2048, 4096, 8192, 16384,
32768, 65536, 131072, 262144, 524288, 1048576, 2097152,
4194304, 8388608, 16777216, 33554432, 67108864, 134217728,
268435456, 536870912, 1073741824, 2147483648U};
*/
stringHashtable *h = (stringHashtable*)malloc(sizeof(stringHashtable));
hashNumberType
tableSize,
i,
primeTableLength = sizeof(initTable)/sizeof(initTable[0]),
maxSize = (hashNumberType)-1;
assert(n <= maxSize);
i = 0;
while(initTable[i] < n && i < primeTableLength)
i++;
assert(i < primeTableLength);
tableSize = initTable[i];
h->table = (stringEntry**)calloc(tableSize, sizeof(stringEntry*));
h->tableSize = tableSize;
return h;
}
static hashNumberType hashString(char *p, hashNumberType tableSize)
{
hashNumberType h = 0;
for(; *p; p++)
h = 31 * h + *p;
return (h % tableSize);
}
void addword(char *s, stringHashtable *h, int nodeNumber)
{
hashNumberType position = hashString(s, h->tableSize);
stringEntry *p = h->table[position];
for(; p!= NULL; p = p->next)
{
if(strcmp(s, p->word) == 0)
return;
}
p = (stringEntry *)malloc(sizeof(stringEntry));
assert(p);
p->nodeNumber = nodeNumber;
p->word = (char *)malloc((strlen(s) + 1) * sizeof(char));
strcpy(p->word, s);
p->next = h->table[position];
h->table[position] = p;
}
int lookupWord(char *s, stringHashtable *h)
{
hashNumberType position = hashString(s, h->tableSize);
stringEntry *p = h->table[position];
for(; p!= NULL; p = p->next)
{
if(strcmp(s, p->word) == 0)
return p->nodeNumber;
}
return -1;
}
int countTips(nodeptr p, int numsp)
{
if(isTip(p->number, numsp))
return 1;
{
nodeptr q;
int tips = 0;
q = p->next;
while(q != p)
{
tips += countTips(q->back, numsp);
q = q->next;
}
return tips;
}
}
static double getBranchLength(tree *tr, int perGene, nodeptr p)
{
double
z = 0.0,
x = 0.0;
assert(perGene != NO_BRANCHES);
if(!tr->multiBranch)
{
assert(tr->fracchange != -1.0);
z = p->z[0];
if (z < zmin)
z = zmin;
x = -log(z) * tr->fracchange;
}
else
{
if(perGene == SUMMARIZE_LH)
{
int
i;
double
avgX = 0.0;
for(i = 0; i < tr->numBranches; i++)
{
assert(tr->partitionContributions[i] != -1.0);
assert(tr->fracchanges[i] != -1.0);
z = p->z[i];
if(z < zmin)
z = zmin;
x = -log(z) * tr->fracchanges[i];
avgX += x * tr->partitionContributions[i];
}
x = avgX;
}
else
{
assert(tr->fracchanges[perGene] != -1.0);
assert(perGene >= 0 && perGene < tr->numBranches);
z = p->z[perGene];
if(z < zmin)
z = zmin;
x = -log(z) * tr->fracchanges[perGene];
}
}
return x;
}
static char *Tree2StringREC(char *treestr, tree *tr, nodeptr p, boolean printBranchLengths, boolean printNames,
boolean printLikelihood, boolean rellTree, boolean finalPrint, int perGene, boolean branchLabelSupport, boolean printSHSupport)
{
char *nameptr;
if(isTip(p->number, tr->rdta->numsp))
{
if(printNames)
{
nameptr = tr->nameList[p->number];
sprintf(treestr, "%s", nameptr);
}
else
sprintf(treestr, "%d", p->number);
while (*treestr) treestr++;
}
else
{
*treestr++ = '(';
treestr = Tree2StringREC(treestr, tr, p->next->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport);
*treestr++ = ',';
treestr = Tree2StringREC(treestr, tr, p->next->next->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport);
if(p == tr->start->back)
{
*treestr++ = ',';
treestr = Tree2StringREC(treestr, tr, p->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport);
}
*treestr++ = ')';
}
if(p == tr->start->back)
{
if(printBranchLengths && !rellTree)
sprintf(treestr, ":0.0;\n");
else
sprintf(treestr, ";\n");
}
else
{
if(rellTree || branchLabelSupport || printSHSupport)
{
if(( !isTip(p->number, tr->rdta->numsp)) &&
( !isTip(p->back->number, tr->rdta->numsp)))
{
assert(p->bInf != (branchInfo *)NULL);
if(rellTree)
sprintf(treestr, "%d:%8.20f", p->bInf->support, p->z[0]);
if(branchLabelSupport)
sprintf(treestr, ":%8.20f[%d]", p->z[0], p->bInf->support);
if(printSHSupport)
sprintf(treestr, ":%8.20f[%d]", getBranchLength(tr, perGene, p), p->bInf->support);
}
else
{
if(rellTree || branchLabelSupport)
sprintf(treestr, ":%8.20f", p->z[0]);
if(printSHSupport)
sprintf(treestr, ":%8.20f", getBranchLength(tr, perGene, p));
}
}
else
{
if(printBranchLengths)
sprintf(treestr, ":%8.20f", getBranchLength(tr, perGene, p));
else
sprintf(treestr, "%s", "\0");
}
}
while (*treestr) treestr++;
return treestr;
}
static void collectSubtrees(tree *tr, nodeptr *subtrees, int *count, int ogn)
{
int i;
for(i = tr->mxtips + 1; i <= tr->mxtips + tr->mxtips - 2; i++)
{
nodeptr p, q;
p = tr->nodep[i];
if(countTips(p, tr->rdta->numsp) == ogn)
{
subtrees[*count] = p;
*count = *count + 1;
}
q = p->next;
while(q != p)
{
if(countTips(q, tr->rdta->numsp) == ogn)
{
subtrees[*count] = q;
*count = *count + 1;
}
q = q->next;
}
}
}
static void checkOM(nodeptr p, int *n, int *c, tree *tr)
{
if(isTip(p->number, tr->rdta->numsp))
{
n[*c] = p->number;
*c = *c + 1;
}
else
{
nodeptr q = p->next;
while(q != p)
{
checkOM(q->back, n, c, tr);
q = q->next;
}
}
}
static char *rootedTreeREC(char *treestr, tree *tr, nodeptr p, boolean printBranchLengths, boolean printNames,
boolean printLikelihood, boolean rellTree,
boolean finalPrint, analdef *adef, int perGene, boolean branchLabelSupport, boolean printSHSupport)
{
char *nameptr;
if(isTip(p->number, tr->rdta->numsp))
{
if(printNames)
{
nameptr = tr->nameList[p->number];
sprintf(treestr, "%s", nameptr);
}
else
sprintf(treestr, "%d", p->number);
while (*treestr) treestr++;
}
else
{
*treestr++ = '(';
treestr = rootedTreeREC(treestr, tr, p->next->back, printBranchLengths, printNames, printLikelihood,
rellTree, finalPrint, adef, perGene, branchLabelSupport, printSHSupport);
*treestr++ = ',';
treestr = rootedTreeREC(treestr, tr, p->next->next->back, printBranchLengths, printNames, printLikelihood,
rellTree, finalPrint, adef, perGene, branchLabelSupport, printSHSupport);
*treestr++ = ')';
}
if(rellTree || branchLabelSupport || printSHSupport)
{
if(( !isTip(p->number, tr->rdta->numsp)) &&
( !isTip(p->back->number, tr->rdta->numsp)))
{
assert(p->bInf != (branchInfo *)NULL);
if(rellTree)
sprintf(treestr, "%d:%8.20f", p->bInf->support, p->z[0]);
if(branchLabelSupport)
sprintf(treestr, ":%8.20f[%d]", p->z[0], p->bInf->support);
if(printSHSupport)
sprintf(treestr, ":%8.20f[%d]", getBranchLength(tr, perGene, p), p->bInf->support);
}
else
{
if(rellTree || branchLabelSupport)
sprintf(treestr, ":%8.20f", p->z[0]);
if(printSHSupport)
sprintf(treestr, ":%8.20f", getBranchLength(tr, perGene, p));
}
}
else
{
if(printBranchLengths)
sprintf(treestr, ":%8.20f", getBranchLength(tr, perGene, p));
else
sprintf(treestr, "%s", "\0");
}
while (*treestr) treestr++;
return treestr;
}
static char *rootedTree(char *treestr, tree *tr, nodeptr p, boolean printBranchLengths, boolean printNames,
boolean printLikelihood, boolean rellTree,
boolean finalPrint, analdef *adef, int perGene, boolean branchLabelSupport, boolean printSHSupport)
{
double oldz[NUM_BRANCHES];
int i;
for(i = 0; i < tr->numBranches; i++)
oldz[i] = p->z[i];
if(rellTree)
{
p->z[0] = p->back->z[0] = oldz[0] * 0.5;
/*printf("%f\n", p->z[0]);*/
}
else
{
if(printBranchLengths)
{
double rz, z;
assert(perGene != NO_BRANCHES);
if(!tr->multiBranch)
{
assert(tr->fracchange != -1.0);
z = -log(p->z[0]) * tr->fracchange;
rz = exp(-(z * 0.5)/ tr->fracchange);
p->z[0] = p->back->z[0] = rz;
}
else
{
if(perGene == SUMMARIZE_LH)
{
int i;
for(i = 0; i < tr->numBranches; i++)
{
assert(tr->fracchanges[i] != -1.0);
z = -log(p->z[i]) * tr->fracchanges[i];
rz = exp(-(z * 0.5)/ tr->fracchanges[i]);
p->z[i] = p->back->z[i] = rz;
}
}
else
{
assert(tr->fracchanges[perGene] != -1.0);
assert(perGene >= 0 && perGene < tr->numBranches);
z = -log(p->z[perGene]) * tr->fracchanges[perGene];
rz = exp(-(z * 0.5)/ tr->fracchanges[perGene]);
p->z[perGene] = p->back->z[perGene] = rz;
}
}
}
}
*treestr = '(';
treestr++;
treestr = rootedTreeREC(treestr, tr, p, printBranchLengths, printNames, printLikelihood, rellTree, finalPrint,
adef, perGene, branchLabelSupport, printSHSupport);
*treestr = ',';
treestr++;
treestr = rootedTreeREC(treestr, tr, p->back, printBranchLengths, printNames, printLikelihood, rellTree, finalPrint,
adef, perGene, branchLabelSupport, printSHSupport);
sprintf(treestr, ");\n");
while (*treestr) treestr++;
for(i = 0; i < tr->numBranches; i++)
p->z[i] = p->back->z[i] = oldz[i];
return treestr;
}
char *Tree2String(char *treestr, tree *tr, nodeptr p, boolean printBranchLengths, boolean printNames, boolean printLikelihood,
boolean rellTree,
boolean finalPrint, analdef *adef, int perGene, boolean branchLabelSupport, boolean printSHSupport)
{
if(rellTree)
assert(!branchLabelSupport && !printSHSupport);
if(branchLabelSupport)
assert(!rellTree && !printSHSupport);
if(printSHSupport)
assert(!branchLabelSupport && !rellTree);
if(finalPrint && adef->outgroup)
{
nodeptr startNode = tr->start;
if(tr->numberOfOutgroups > 1)
{
nodeptr root;
nodeptr *subtrees = (nodeptr *)malloc(sizeof(nodeptr) * tr->mxtips);
int i, k, count = 0;
int *nodeNumbers = (int*)malloc(sizeof(int) * tr->numberOfOutgroups);
int *foundVector = (int*)malloc(sizeof(int) * tr->numberOfOutgroups);
boolean monophyletic = FALSE;
collectSubtrees(tr, subtrees, &count, tr->numberOfOutgroups);
/*printf("Found %d subtrees of size %d\n", count, tr->numberOfOutgroups);*/
for(i = 0; (i < count) && (!monophyletic); i++)
{
int l, sum, nc = 0;
for(k = 0; k < tr->numberOfOutgroups; k++)
{
nodeNumbers[k] = -1;
foundVector[k] = 0;
}
checkOM(subtrees[i], nodeNumbers, &nc, tr);
for(l = 0; l < tr->numberOfOutgroups; l++)
for(k = 0; k < tr->numberOfOutgroups; k++)
{
if(nodeNumbers[l] == tr->outgroupNums[k])
foundVector[l] = 1;
}
sum = 0;
for(l = 0; l < tr->numberOfOutgroups; l++)
sum += foundVector[l];
if(sum == tr->numberOfOutgroups)
{
root = subtrees[i];
tr->start = root;
/*printf("outgroups are monphyletic!\n");*/
monophyletic = TRUE;
}
else
{
if(sum > 0)
{
/*printf("outgroups are NOT monophyletic!\n");*/
monophyletic = FALSE;
}
}
}
if(!monophyletic)
{
printf("WARNING, outgroups are not monophyletic, using first outgroup \"%s\"\n", tr->nameList[tr->outgroupNums[0]]);
printf("from the list to root the tree!\n");
{
FILE *infoFile = myfopen(infoFileName, "ab");
fprintf(infoFile, "\nWARNING, outgroups are not monophyletic, using first outgroup \"%s\"\n", tr->nameList[tr->outgroupNums[0]]);
fprintf(infoFile, "from the list to root the tree!\n");
fclose(infoFile);
}
tr->start = tr->nodep[tr->outgroupNums[0]];
rootedTree(treestr, tr, tr->start->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, adef, perGene, branchLabelSupport, printSHSupport);
}
else
{
if(isTip(tr->start->number, tr->rdta->numsp))
{
printf("Outgroup-Monophyly ERROR; tr->start is a tip \n");
errorExit(-1);
}
if(isTip(tr->start->back->number, tr->rdta->numsp))
{
printf("Outgroup-Monophyly ERROR; tr->start is a tip \n");
errorExit(-1);
}
rootedTree(treestr, tr, tr->start->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, adef, perGene, branchLabelSupport, printSHSupport);
}
free(foundVector);
free(nodeNumbers);
free(subtrees);
}
else
{
tr->start = tr->nodep[tr->outgroupNums[0]];
rootedTree(treestr, tr, tr->start->back, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, adef, perGene, branchLabelSupport, printSHSupport);
}
tr->start = startNode;
}
else
Tree2StringREC(treestr, tr, p, printBranchLengths, printNames, printLikelihood, rellTree,
finalPrint, perGene, branchLabelSupport, printSHSupport);
while (*treestr) treestr++;
return treestr;
}
void printTreePerGene(tree *tr, analdef *adef, char *fileName, char *permission)
{
FILE *treeFile;
char extendedTreeFileName[1024];
char buf[16];
int i;
assert(adef->perGeneBranchLengths);
for(i = 0; i < tr->numBranches; i++)
{
strcpy(extendedTreeFileName, fileName);
sprintf(buf,"%d", i);
strcat(extendedTreeFileName, ".PARTITION.");
strcat(extendedTreeFileName, buf);
/*printf("Partitiuon %d file %s\n", i, extendedTreeFileName);*/
Tree2String(tr->tree_string, tr, tr->start->back, TRUE, TRUE, FALSE, FALSE, TRUE, adef, i, FALSE, FALSE);
treeFile = myfopen(extendedTreeFileName, permission);
fprintf(treeFile, "%s", tr->tree_string);
fclose(treeFile);
}
}
/*=======================================================================*/
/* Read a tree from a file */
/*=======================================================================*/
/* 1.0.A Processing of quotation marks in comment removed
*/
static int treeFinishCom (FILE *fp, char **strp)
{
int ch;
while ((ch = getc(fp)) != EOF && ch != ']') {
if (strp != NULL) *(*strp)++ = ch; /* save character */
if (ch == '[') { /* nested comment; find its end */
if ((ch = treeFinishCom(fp, strp)) == EOF) break;
if (strp != NULL) *(*strp)++ = ch; /* save closing ] */
}
}
if (strp != NULL) **strp = '\0'; /* terminate string */
return ch;
} /* treeFinishCom */
static int treeGetCh (FILE *fp) /* get next nonblank, noncomment character */
{ /* treeGetCh */
int ch;
while ((ch = getc(fp)) != EOF) {
if (whitechar(ch)) ;
else if (ch == '[') { /* comment; find its end */
if ((ch = treeFinishCom(fp, (char **) NULL)) == EOF) break;
}
else break;
}
return ch;
} /* treeGetCh */
static boolean treeLabelEnd (int ch)
{
switch (ch)
{
case EOF:
case '\0':
case '\t':
case '\n':
case '\r':
case ' ':
case ':':
case ',':
case '(':
case ')':
case ';':
return TRUE;
default:
break;
}
return FALSE;
}
static boolean treeGetLabel (FILE *fp, char *lblPtr, int maxlen)
{
int ch;
boolean done, quoted, lblfound;
if (--maxlen < 0)
lblPtr = (char *) NULL;
else
if (lblPtr == NULL)
maxlen = 0;
ch = getc(fp);
done = treeLabelEnd(ch);
lblfound = ! done;
quoted = (ch == '\'');
if (quoted && ! done)
{
ch = getc(fp);
done = (ch == EOF);
}
while (! done)
{
if (quoted)
{
if (ch == '\'')
{
ch = getc(fp);
if (ch != '\'')
break;
}
}
else
if (treeLabelEnd(ch)) break;
if (--maxlen >= 0) *lblPtr++ = ch;
ch = getc(fp);
if (ch == EOF) break;
}
if (ch != EOF) (void) ungetc(ch, fp);
if (lblPtr != NULL) *lblPtr = '\0';
return lblfound;
}
static boolean treeFlushLabel (FILE *fp)
{
return treeGetLabel(fp, (char *) NULL, (int) 0);
}
static int treeFindTipByLabelString(char *str, tree *tr)
{
int lookup = lookupWord(str, tr->nameHash);
if(lookup > 0)
{
assert(! tr->nodep[lookup]->back);
return lookup;
}
else
{
printf("ERROR: Cannot find tree species: %s\n", str);
return 0;
}
}
static int treeFindTipName(FILE *fp, tree *tr)
{
char str[nmlngth+2];
int n;
if(treeGetLabel(fp, str, nmlngth+2))
n = treeFindTipByLabelString(str, tr);
else
n = 0;
return n;
}
static void treeEchoContext (FILE *fp1, FILE *fp2, int n)
{ /* treeEchoContext */
int ch;
boolean waswhite;
waswhite = TRUE;
while (n > 0 && ((ch = getc(fp1)) != EOF)) {
if (whitechar(ch)) {
ch = waswhite ? '\0' : ' ';
waswhite = TRUE;
}
else {
waswhite = FALSE;
}
if (ch > '\0') {putc(ch, fp2); n--;}
}
} /* treeEchoContext */
static boolean treeProcessLength (FILE *fp, double *dptr)
{
int ch;
if ((ch = treeGetCh(fp)) == EOF) return FALSE; /* Skip comments */
(void) ungetc(ch, fp);
if (fscanf(fp, "%lf", dptr) != 1) {
printf("ERROR: treeProcessLength: Problem reading branch length\n");
treeEchoContext(fp, stdout, 40);
printf("\n");
return FALSE;
}
return TRUE;
}
static int treeFlushLen (FILE *fp)
{
double dummy;
int ch;
ch = treeGetCh(fp);
if (ch == ':')
{
ch = treeGetCh(fp);
ungetc(ch, fp);
if(!treeProcessLength(fp, & dummy)) return 0;
return 1;
}
if (ch != EOF) (void) ungetc(ch, fp);
return 1;
}
static boolean treeNeedCh (FILE *fp, int c1, char *where)
{
int c2;
if ((c2 = treeGetCh(fp)) == c1) return TRUE;
printf("ERROR: Expecting '%c' %s tree; found:", c1, where);
if (c2 == EOF)
{
printf("End-of-File");
}
else
{
ungetc(c2, fp);
treeEchoContext(fp, stdout, 40);
}
putchar('\n');
if(c1 == ':')
printf("RAxML may be expecting to read a tree that contains branch lengths\n");
return FALSE;
}
static boolean addElementLen (FILE *fp, tree *tr, nodeptr p, boolean readBranchLengths, boolean readNodeLabels, int *lcount)
{
nodeptr q;
int n, ch, fres;
if ((ch = treeGetCh(fp)) == '(')
{
n = (tr->nextnode)++;
if (n > 2*(tr->mxtips) - 2)
{
if (tr->rooted || n > 2*(tr->mxtips) - 1)
{
printf("ERROR: Too many internal nodes. Is tree rooted?\n");
printf(" Deepest splitting should be a trifurcation.\n");
return FALSE;
}
else
{
assert(!readNodeLabels);
tr->rooted = TRUE;
}
}
q = tr->nodep[n];
if (! addElementLen(fp, tr, q->next, readBranchLengths, readNodeLabels, lcount)) return FALSE;
if (! treeNeedCh(fp, ',', "in")) return FALSE;
if (! addElementLen(fp, tr, q->next->next, readBranchLengths, readNodeLabels, lcount)) return FALSE;
if (! treeNeedCh(fp, ')', "in")) return FALSE;
if(readNodeLabels)
{
char label[64];
int support;
if(treeGetLabel (fp, label, 10))
{
int val = sscanf(label, "%d", &support);
assert(val == 1);
/*printf("LABEL %s Number %d\n", label, support);*/
p->support = q->support = support;
/*printf("%d %d %d %d\n", p->support, q->support, p->number, q->number);*/
assert(p->number > tr->mxtips && q->number > tr->mxtips);
*lcount = *lcount + 1;
}
}
else
(void) treeFlushLabel(fp);
}
else
{
ungetc(ch, fp);
if ((n = treeFindTipName(fp, tr)) <= 0) return FALSE;
q = tr->nodep[n];
if (tr->start->number > n) tr->start = q;
(tr->ntips)++;
}
if(readBranchLengths)
{
double branch;
if (! treeNeedCh(fp, ':', "in")) return FALSE;
if (! treeProcessLength(fp, &branch)) return FALSE;
/*printf("Branch %8.20f %d\n", branch, tr->numBranches);*/
hookup(p, q, &branch, tr->numBranches);
}
else
{
fres = treeFlushLen(fp);
if(!fres) return FALSE;
hookupDefault(p, q, tr->numBranches);
}
return TRUE;
}
static nodeptr uprootTree (tree *tr, nodeptr p, boolean readBranchLengths, boolean readConstraint)
{