void main (int argc, char*argv[])
{
int lline=32000, i,j, ch, jeffnode, inode;
char line[32000], mcmcf[96]="o.multidivtime";
FILE *fmcmc;
double t;
puts("Usage:\n\tTreeTimeJeff <MultidivtimeOutputFile>\n");
if(argc>1) strcpy(mcmcf, argv[1]);
fmcmc=gfopen(mcmcf, "r");
/* Read root node number */
for( ; ; ) {
if(fgets(line, lline, fmcmc) == NULL) error2("EOF mcmc file");
if(strstr(line, "Root node number of master tree is")==NULL) continue;
sscanf(line+35, "%d", &j);
com.ns=j/2+1;
break;
}
printf("Tree has %d taxa.\n\n", com.ns);
/* read tree. JeffNode read into [].branch */
for(; ; ) {
ch=fgetc(fmcmc);
if(ch==EOF) error2("EOF treefile");
if(ch=='(')
{ ungetc(ch,fmcmc); break; }
}
ReadTreeN(fmcmc, &i, &j, 2, 0);
OutTreeN(F0,1,0); FPN(F0); FPN(F0);
/* read posterior time estimates */
for(i=0; i<tree.nnode; i++) nodes[i].age=0;
for( ; ; ) {
if(fgets(line, lline, fmcmc) == NULL) error2("EOF mcmc file");
if(strstr(line, "Actual time node")==NULL) continue;
sscanf(line+17, "%d =%lf", &jeffnode, &t);
if(jeffnode<com.ns) {
if(t>0) nodes[inode].age=t;
}
else {
inode=tree.nnode-1+com.ns-jeffnode;
printf("JeffNode %3d ZihengNode %3d time %9.6f\n", jeffnode,inode+1,t);
nodes[inode].age=t;
if(inode==com.ns) break;
if(jeffnode-nodes[inode].branch != 0)
printf(" node number error. ");
}
}
for(i=0; i<tree.nnode; i++)
if(i!=tree.root) nodes[i].branch=nodes[nodes[i].father].age-nodes[i].age;
FPN(F0); OutTreeN(F0,1,1); FPN(F0);
fclose(fmcmc);
exit(0);
}
int ListTrees (FILE* fout, int ns, int rooted)
{
/* list trees by adding species, works fine with large ns
*/
int NTrees, NTreeRoot=3;
int i, Ib[NS-2], ns1=ns+rooted, nM=ns1-3, finish;
if(com.ns<=12) {
printf ("%20s%20s%20s\n", "Taxa", "Unrooted trees", "Rooted trees");
for (i=4,NTrees=1; i<=com.ns; i++)
printf ("%20d%20d%20d\n", i, (NTrees*=2*i-5), (NTreeRoot*=2*i-3));
fprintf (fout, "%10d %10d\n", com.ns, (!rooted?NTrees:NTreeRoot));
}
if(com.ns<=26) {
for (i=0; i<com.ns; i++)
sprintf(com.spname[i], "%d", i+1);
}
for (i=0;i<nM;i++) Ib[i]=0;
for (NTrees=0; ; ) {
MakeTreeIb(ns, Ib, rooted);
OutTreeN(fout, (com.ns<=26), 0);
if(rooted) fprintf(fout, " [%7d %6d LHs]\n", NTrees++, CountLHsTree());
else fprintf(fout, " [%7d]\n", NTrees++);
for (i=nM-1,Ib[nM-1]++,finish=0; i>=0; i--) {
if (Ib[i]<2*i+3) break;
if (i==0) {
finish=1;
break;
}
Ib[i]=0; Ib[i-1]++;
}
if (finish) break;
}
FPN(fout);
return (0);
}
int main (int argc, char*argv[])
{
char *MCctlf=NULL, outf[512]="evolver.out", treefile[512]="mcmc.txt", mastertreefile[512]="\0";
int i, option=-1, ntree=1,rooted, BD=0, gotoption=0, pick1tree=-1;
double bfactor=1, birth=-1,death=-1,sample=-1,mut=-1, *space;
FILE *fout=gfopen(outf,"w");
printf("EVOLVER in %s\n", pamlVerStr);
com.alpha=0; com.cleandata=1; com.model=0; com.NSsites=0;
if(argc>1) {
gotoption=1; sscanf(argv[1], "%d", &option);
}
if(argc==1)
printf("Results for options 1-4 & 8 go into %s\n",outf);
else if(option!=5 && option!=6 && option!=7 && option!=9) {
puts("Usage: \n\tevolver \n\tevolver option# MyDataFile"); exit(-1);
}
if(option>=4 && option<=6)
MCctlf = argv[2];
else if(option==9) {
strcpy(treefile, argv[2]);
if(argc>3) strcpy(mastertreefile, argv[3]);
if(argc>4) sscanf(argv[4], "%d", &pick1tree);
}
#if defined (CodonNSbranches)
option=6; com.model=1;
MCctlf = (argc==3 ? argv[2] : "MCcodonNSbranches.dat");
gotoption = 1;
#elif defined (CodonNSsites)
option=6; com.NSsites=3;
MCctlf = (argc==3 ? argv[2] : "MCcodonNSsites.dat");
gotoption = 1;
#elif defined (CodonNSbranchsites)
option=6; com.model=1; com.NSsites=3;
MCctlf = (argc==3 ? argv[2] : "MCcodonNSbranchsites.dat");
gotoption = 1;
#endif
if(!gotoption) {
for(; ;) {
fflush(fout);
printf("\n\t(1) Get random UNROOTED trees?\n");
printf("\t(2) Get random ROOTED trees?\n");
printf("\t(3) List all UNROOTED trees?\n");
printf("\t(4) List all ROOTED trees?\n");
printf("\t(5) Simulate nucleotide data sets (use %s)?\n",MCctlf0[0]);
printf("\t(6) Simulate codon data sets (use %s)?\n",MCctlf0[1]);
printf("\t(7) Simulate amino acid data sets (use %s)?\n",MCctlf0[2]);
printf("\t(8) Calculate identical bi-partitions between trees?\n");
printf("\t(9) Calculate clade support values (evolver 9 treefile mastertreefile <pick1tree>)?\n");
printf("\t(11) Label clades?\n");
printf("\t(0) Quit?\n");
option = 9;
scanf("%d", &option);
if(option==0) exit(0);
if(option>=5 && option<=7) break;
if(option<5) {
printf ("No. of species: ");
scanf ("%d", &com.ns);
}
if(com.ns>NS) error2 ("Too many species. Raise NS.");
if((space=(double*)malloc(10000*sizeof(double)))==NULL) error2("oom");
rooted = !(option%2);
if(option<3) {
printf("\nnumber of trees & random number seed? ");
scanf("%d%d", &ntree, &i);
SetSeed(i, 1);
printf ("Want branch lengths from the birth-death process (0/1)? ");
scanf ("%d", &BD);
}
if(option<=4) {
if(com.ns<3) error2("no need to do this?");
i = (com.ns*2-1)*sizeof(struct TREEN);
if((nodes=(struct TREEN*)malloc(i)) == NULL)
error2("oom");
}
switch (option) {
case(1): /* random UNROOTED trees */
case(2): /* random ROOTED trees */
/* default names */
if(com.ns<=52)
for(i=0; i<com.ns; i++) sprintf(com.spname[i], "%c", (i<26 ? 'A'+i : 'a'+i-26));
else
for(i=0; i<com.ns; i++) sprintf(com.spname[i], "S%d", i+1);
if(BD) {
printf ("\nbirth rate, death rate, sampling fraction, and ");
printf ("mutation rate (tree height)?\n");
scanf ("%lf%lf%lf%lf", &birth, &death, &sample, &mut);
}
for(i=0;i<ntree;i++) {
RandomLHistory (rooted, space);
if(BD)
BranchLengthBD (1, birth, death, sample, mut);
if(com.ns<20&&ntree<10) { OutTreeN(F0, 0, BD); puts("\n"); }
OutTreeN(fout, 1, BD); FPN(fout);
}
/*
for (i=0; i<com.ns-2-!rooted; i++)
Ib[i] = (int)((3.+i)*rndu());
MakeTreeIb (com.ns, Ib, rooted);
*/
break;
case(3):
case(4):
ListTrees(fout, com.ns, rooted);
break;
case(8): TreeDistances(fout); break;
case(9):
printf("tree file names? ");
scanf("%s%s", treefile, mastertreefile);
break;
case(10): between_f_and_x(); break;
case(11): LabelClades(fout); break;
default: exit(0);
}
}
}
if(option>=5 && option<=7) {
com.seqtype = option-5; /* 0, 1, 2 for bases, codons, & amino acids */
Simulate(MCctlf ? MCctlf : MCctlf0[option-5]);
}
else if(option==9) {
CladeSupport(fout, treefile, mastertreefile, pick1tree);
/* CladeMrBayesProbabilities("/papers/BPPJC3sB/Karol.trees"); */
}
return(0);
}
void TreeDistances (FILE* fout)
{
/* I think this is broken after i changed the routine Tree2Partition().
*/
int i,j,ntree, k,*nib, parti2B[NS], nsame, IBsame[NS],nIBsame[NS], lpart=0;
char treef[64]="5s.all.trees", *partition;
FILE *ftree;
double psame, mp, vp;
/*
TreeDistanceDistribution(fout);
*/
puts("\nNumber of identical bi-partitions between trees.\nTree file name?");
scanf ("%s", treef);
ftree=gfopen (treef,"r");
fscanf (ftree, "%d%d", &com.ns, &ntree);
printf("%2d sequences %2d trees.\n", com.ns, ntree);
i=(com.ns*2-1)*sizeof(struct TREEN);
if((nodes=(struct TREEN*)malloc(i))==NULL) error2("oom");
if(ntree<2) error2("ntree");
printf ("\n%d species, %d trees\n", com.ns, ntree);
puts("\n\t1: first vs. rest?\n\t2: all pairwise comparisons?\n");
k=2;
scanf("%d", &k);
lpart=(com.ns-1)*com.ns*sizeof(char);
i=(k==1?2:ntree)*lpart;
printf("\n%d bytes of space requested.\n", i);
partition=(char*)malloc(i);
nib=(int*)malloc(ntree*sizeof(int));
if (partition==NULL || nib==NULL) error2("out of memory");
if(k==2) { /* pairwise comparisons */
fputs("Number of identical bi-partitions in pairwise comparisons\n",fout);
for (i=0; i<ntree; i++) {
ReadTreeN (ftree, &j, &k, 0, 1);
nib[i]=tree.nbranch-com.ns;
Tree2Partition(partition+i*lpart);
}
for (i=0; i<ntree; i++,FPN(F0),FPN(fout)) {
printf("%2d (%2d):", i+1,nib[i]);
fprintf(fout,"%2d (%2d):", i+1,nib[i]);
for (j=0; j<i; j++) {
nsame=NSameBranch(partition+i*lpart,partition+j*lpart, nib[i],nib[j],IBsame);
printf(" %2d", nsame);
fprintf(fout," %2d", nsame);
}
}
}
else { /* first vs. others */
ReadTreeN (ftree, &j, &k, 0, 1);
nib[0]=tree.nbranch-com.ns;
if (nib[0]==0) error2("1st tree is a star tree..");
Tree2Partition (partition);
fputs ("Comparing the first tree with the others\nFirst tree:\n",fout);
OutTreeN(fout,0,0); FPN(fout); OutTreeB(fout); FPN(fout);
fputs ("\nInternal branches in the first tree:\n",fout);
FOR(i,nib[0]) {
k=parti2B[i];
fprintf(fout,"%3d (%2d..%-2d): ( ",
i+1,tree.branches[k][0]+1,tree.branches[k][1]+1);
FOR(j,com.ns) if(partition[i*com.ns+j]) fprintf(fout,"%d ",j+1);
fputs(")\n",fout);
}
if(nodes[tree.root].nson<=2)
fputs("\nRooted tree, results may not be correct.\n",fout);
fputs("\nCorrect internal branches compared with the 1st tree:\n",fout);
FOR(k,nib[0]) nIBsame[k]=0;
for (i=1,mp=vp=0; i<ntree; i++,FPN(fout)) {
ReadTreeN (ftree, &j, &k, 0, 1);
nib[1]=tree.nbranch-com.ns;
Tree2Partition(partition+lpart);
nsame=NSameBranch (partition,partition+lpart, nib[0],nib[1],IBsame);
psame=nsame/(double)nib[0];
FOR(k,nib[0]) nIBsame[k]+=IBsame[k];
fprintf(fout,"1 vs. %3d: %4d: ", i+1,nsame);
FOR(k,nib[0]) if(IBsame[k]) fprintf(fout," %2d", k+1);
printf("1 vs. %5d: %6d/%d %10.4f\n", i+1,nsame,nib[0],psame);
vp += square(psame - mp)*(i-1.)/i;
mp=(mp*(i-1.) + psame)/i;
}
vp=(ntree<=2 ? 0 : sqrt(vp/((ntree-1-1)*(ntree-1.))));
fprintf(fout,"\nmean and S.E. of proportion of identical partitions\n");
fprintf(fout,"between the 1st and all the other %d trees ", ntree-1);
fprintf(fout,"(ignore these if not revelant):\n %.4f +- %.4f\n", mp, vp);
fprintf(fout,"\nNumbers of times, out of %d, ", ntree-1);
fprintf(fout,"interior branches of tree 1 are present");
fputs("\n(This may be bootstrap support for nodes in tree 1)\n",fout);
FOR(k,nib[0]) {
i=tree.branches[parti2B[k]][0]+1; j=tree.branches[parti2B[k]][1]+1;
fprintf(fout,"%3d (%2d..%-2d): %6d (%5.1f%%)\n",
k+1,i,j,nIBsame[k],nIBsame[k]*100./(ntree-1.));
}
void LabelClades(FILE *fout)
{
/* This reads in a tree and scan species names to check whether they form a
paraphyletic group and then label the clade.
It assumes that the tree is unrooted, and so goes through two rounds to check
whether the remaining seqs form a monophyletic clade.
*/
FILE *ftree;
int unrooted=1,iclade, sizeclade, mrca, paraphyl, is, imrca, i,j,k, lasts, haslength;
char key[96]="A", treef[64]="/A/F/flu/HA.all.prankcodon.tre", *p,chosen[NS], *endstr="end";
int *anc[NS-1], loc, bitmask, SI=sizeof(int)*8;
int debug;
printf("Tree file name? ");
scanf ("%s", treef);
printf("Treat tree as unrooted (0 no, 1 yes)? ");
scanf ("%d", &unrooted);
ftree = gfopen (treef,"r");
fscanf (ftree, "%d%d", &com.ns, &j);
if(com.ns<=0) error2("need ns in tree file");
debug = (com.ns<20);
i = (com.ns*2-1)*sizeof(struct TREEN);
if((nodes=(struct TREEN*)malloc(i))==NULL) error2("oom");
for(i=0; i<com.ns*2-1; i++) nodes[i].nodeStr = NULL;
for(i=0; i<com.ns-1; i++) {
anc[i] = (int*)malloc((com.ns/SI+1)*sizeof(int));
if(anc[i]==NULL) error2("oom");
}
ReadTreeN(ftree, &haslength, &j, 1, 0);
fclose(ftree);
if(debug) { OutTreeN(F0, 1, PrNodeNum); FPN(F0); }
for(iclade=0; iclade<com.ns-1; iclade++) {
printf("\nString for selecting sequences (followed by non-digit) (end to end)? ");
scanf("%s", key);
if(strcmp(endstr, key) == 0)
break;
for(i=0; i<com.ns; i++)
chosen[i] = '\0';
k = strlen(key);
for(i=0; i<com.ns; i++) {
if( (p=strstr(com.spname[i], key))
&& !isdigit(p[k]) )
chosen[i] = 1;
}
/*
for(i=0; i<com.ns; i++)
if(strstr(com.spname[i], key)) chosen[i] = 1;
*/
/* look for MRCA, going through two rounds, assuming unrooted tree */
for(imrca=0; imrca<1+unrooted; imrca++) {
if(imrca)
for(i=0; i<com.ns; i++) chosen[i] = 1 - chosen[i];
for(i=0,sizeclade=0; i<com.ns; i++)
if(chosen[i]) {
sizeclade ++;
lasts = i;
}
if(sizeclade <= 1 || sizeclade >= com.ns-1) {
puts("unable to form a clade. <2 seqs.");
break;
}
for(i=0; i<com.ns-1; i++) for(j=0; j<com.ns/SI+1; j++)
anc[i][j] = 0;
for(is=0; is<com.ns; is++) {
if(chosen[is]==0) continue;
loc = is/SI; bitmask = 1 << (is%SI);
for(j=nodes[is].father; j!=-1; j=nodes[j].father) {
anc[j-com.ns][loc] |= bitmask;
if(is==lasts) {
for(i=0,k=0; i<com.ns; i++)
if(anc[j-com.ns][i/SI] & (1<<(i%SI)))
k ++;
if(k==sizeclade) {
mrca = j; break;
}
}
}
}
if(imrca==0 && mrca!=tree.root) /* 1st round is enough */
break;
}
if(sizeclade <= 1 || sizeclade >= com.ns-1 || mrca==tree.root) {
printf("Unable to label. Ignored.");
continue;
}
if(debug)
for(is=0; is<com.ns-1; is++) {
printf("\nnode %4d: ", is+com.ns);
for(j=0; j<com.ns; j++) {
loc = j/SI; bitmask = 1 << (j%SI);
printf(" %d", (anc[is][loc] & bitmask) != 0);
}
}
printf("\nClade #%d (%s): %d seqs selected, MRCA is %d\n", iclade+1, key, sizeclade, mrca+1);
for(is=0,paraphyl=0; is<com.ns; is++) {
if(chosen[is] == 0)
for(j=nodes[is].father; j!=-1; j=nodes[j].father)
if(j==mrca) { paraphyl++; break; }
}
if(paraphyl)
printf("\nThis clade is paraphyletic, & includes %d other sequences\n", paraphyl);
nodes[mrca].label = iclade+1;
if(debug) OutTreeN(F0, 1, haslength|PrLabel);
}
for(i=0; i<com.ns-1; i++) free(anc[i]);
OutTreeN(fout, 1, haslength|PrLabel); FPN(fout);
printf("Printed final tree with labels in evolver.out\n");
exit(0);
}
