void getoptions()
{ /* interactively set options */
long inseed0, loopcount;
Char ch;
boolean done;
fprintf(outfile, "\nContinuous character Maximum Likelihood");
fprintf(outfile, " method version %s\n\n",VERSION);
putchar('\n');
global = false;
jumble = false;
njumble = 1;
lengths = false;
outgrno = 1;
outgropt = false;
all = false;
contchars = false;
trout = true;
usertree = false;
printdata = false;
progress = true;
treeprint = true;
loopcount = 0;
do {
cleerhome();
printf("\nContinuous character Maximum Likelihood");
printf(" method version %s\n\n",VERSION);
printf("Settings for this run:\n");
printf(" U Search for best tree? %s\n",
(usertree ? "No, use user trees in input" : "Yes"));
if (usertree) {
printf(" L Use lengths from user trees?%s\n",
(lengths ? " Yes" : " No"));
}
printf(" C Gene frequencies or continuous characters? %s\n",
(contchars ? "Continuous characters" : "Gene frequencies"));
if (!contchars)
printf(" A Input file has all alleles at each locus? %s\n",
(all ? "Yes" : "No, one allele missing at each"));
printf(" O Outgroup root? %s %ld\n",
(outgropt ? "Yes, at species number" :
"No, use as outgroup species"),outgrno);
if (!usertree) {
printf(" G Global rearrangements? %s\n",
(global ? "Yes" : "No"));
printf(" J Randomize input order of species?");
if (jumble)
printf(" Yes (seed=%8ld,%3ld times)\n", inseed0, njumble);
else
printf(" No. Use input order\n");
}
printf(" M Analyze multiple data sets?");
if (mulsets)
printf(" Yes, %2ld sets\n", datasets);
else
printf(" No\n");
printf(" 0 Terminal type (IBM PC, ANSI, none)? %s\n",
ibmpc ? "IBM PC" : ansi ? "ANSI" : "(none)");
printf(" 1 Print out the data at start of run %s\n",
(printdata ? "Yes" : "No"));
printf(" 2 Print indications of progress of run %s\n",
(progress ? "Yes" : "No"));
printf(" 3 Print out tree %s\n",
(treeprint ? "Yes" : "No"));
printf(" 4 Write out trees onto tree file? %s\n",
(trout ? "Yes" : "No"));
printf("\n Y to accept these or type the letter for one to change\n");
#ifdef WIN32
phyFillScreenColor();
#endif
fflush(stdout);
scanf("%c%*[^\n]", &ch);
getchar();
uppercase(&ch);
done = (ch == 'Y');
if (!done) {
if (((!usertree) && (strchr("JOUGACM12340", ch) != NULL))
|| (usertree && ((strchr("LOUACM12340", ch) != NULL)))){
switch (ch) {
case 'A':
if (!contchars)
all = !all;
break;
case 'C':
contchars = !contchars;
break;
case 'G':
global = !global;
break;
case 'J':
jumble = !jumble;
if (jumble)
initjumble(&inseed, &inseed0, seed, &njumble);
else njumble = 1;
break;
case 'L':
lengths = !lengths;
break;
case 'O':
outgropt = !outgropt;
if (outgropt)
initoutgroup(&outgrno, spp);
break;
case 'U':
usertree = !usertree;
break;
case 'M':
mulsets = !mulsets;
if (mulsets)
initdatasets(&datasets);
break;
case '0':
initterminal(&ibmpc, &ansi);
break;
case '1':
printdata = !printdata;
break;
case '2':
progress = !progress;
break;
case '3':
treeprint = !treeprint;
break;
case '4':
trout = !trout;
break;
}
} else
printf("Not a possible option!\n");
}
countup(&loopcount, 100);
} while (!done);
} /* getoptions */
void getoptions()
{
/* interactively set options */
long inseed0=0;
Char ch;
boolean done=false;
putchar('\n');
minev = false;
global = false;
jumble = false;
njumble = 1;
lengths = false;
lower = false;
negallowed = false;
outgrno = 1;
outgropt = false;
power = 2.0;
replicates = false;
trout = true;
upper = false;
usertree = false;
printdata = false;
progress = true;
treeprint = true;
do {
cleerhome();
printf("\nFitch-Margoliash method version %s\n\n",VERSION);
printf("Settings for this run:\n");
printf(" D Method (F-M, Minimum Evolution)? %s\n",
(minev ? "Minimum Evolution" : "Fitch-Margoliash"));
printf(" U Search for best tree? %s\n",
(usertree ? "No, use user trees in input file" : "Yes"));
if (usertree) {
printf(" N Use lengths from user trees? %s\n",
(lengths ? "Yes" : "No"));
}
printf(" P Power?%9.5f\n",power);
printf(" - Negative branch lengths allowed? %s\n",
negallowed ? "Yes" : "No");
printf(" O Outgroup root?");
if (outgropt)
printf(" Yes, at species number%3ld\n", outgrno);
else
printf(" No, use as outgroup species%3ld\n", outgrno);
printf(" L Lower-triangular data matrix?");
if (lower)
printf(" Yes\n");
else
printf(" No\n");
printf(" R Upper-triangular data matrix?");
if (upper)
printf(" Yes\n");
else
printf(" No\n");
printf(" S Subreplicates?");
if (replicates)
printf(" Yes\n");
else
printf(" No\n");
if (!usertree) {
printf(" G Global rearrangements?");
if (global)
printf(" Yes\n");
else
printf(" No\n");
printf(" J Randomize input order of species?");
if (jumble)
printf(" Yes (seed =%8ld,%3ld times)\n", inseed0, njumble);
else
printf(" No. Use input order\n");
}
printf(" M Analyze multiple data sets?");
if (mulsets)
printf(" Yes, %2ld sets\n", datasets);
else
printf(" No\n");
printf(" 0 Terminal type (IBM PC, ANSI, none)?");
if (ibmpc)
printf(" IBM PC\n");
if (ansi)
printf(" ANSI\n");
if (!(ibmpc || ansi))
printf(" (none)\n");
printf(" 1 Print out the data at start of run");
if (printdata)
printf(" Yes\n");
else
printf(" No\n");
printf(" 2 Print indications of progress of run");
if (progress)
printf(" Yes\n");
else
printf(" No\n");
printf(" 3 Print out tree");
if (treeprint)
printf(" Yes\n");
else
printf(" No\n");
printf(" 4 Write out trees onto tree file?");
if (trout)
printf(" Yes\n");
else
printf(" No\n");
printf(
"\n Y to accept these or type the letter for one to change\n");
#ifdef WIN32
phyFillScreenColor();
#endif
scanf("%c%*[^\n]", &ch);
getchar();
uppercase(&ch);
done = (ch == 'Y');
if (!done) {
if (strchr("DJOUNPG-LRSM01234",ch) != NULL) {
switch (ch) {
case 'D':
minev = !minev;
if (minev && (!negallowed))
negallowed = true;
break;
case '-':
negallowed = !negallowed;
break;
case 'G':
global = !global;
break;
case 'J':
jumble = !jumble;
if (jumble)
initjumble(&inseed, &inseed0, seed, &njumble);
else njumble = 1;
break;
case 'L':
lower = !lower;
break;
case 'N':
lengths = !lengths;
break;
case 'O':
outgropt = !outgropt;
if (outgropt)
initoutgroup(&outgrno, spp);
break;
case 'P':
initpower(&power);
break;
case 'R':
upper = !upper;
break;
case 'S':
replicates = !replicates;
break;
case 'U':
usertree = !usertree;
break;
case 'M':
mulsets = !mulsets;
if (mulsets)
initdatasets(&datasets);
break;
case '0':
initterminal(&ibmpc, &ansi);
break;
case '1':
printdata = !printdata;
break;
case '2':
progress = !progress;
break;
case '3':
treeprint = !treeprint;
break;
case '4':
trout = !trout;
break;
}
} else
printf("Not a possible option!\n");
}
} while (!done);
} /* getoptions */
void getoptions()
{
/* interactively set options */
long loopcount, loopcount2;
Char ch, ch2;
fprintf(outfile, "\nPenny algorithm, version %s\n",VERSION);
fprintf(outfile, " branch-and-bound to find all");
fprintf(outfile, " most parsimonious trees\n\n");
howoften = often;
howmanny = many;
outgrno = 1;
outgropt = false;
simple = true;
thresh = false;
threshold = spp;
trout = true;
weights = false;
justwts = false;
ancvar = false;
allsokal = false;
allwagner = true;
mixture = false;
printdata = false;
progress = true;
treeprint = true;
stepbox = false;
ancseq = false;
loopcount = 0;
for(;;) {
cleerhome();
printf("\nPenny algorithm, version %s\n",VERSION);
printf(" branch-and-bound to find all most parsimonious trees\n\n");
printf("Settings for this run:\n");
printf(" X Use Mixed method? %s\n",
mixture ? "Yes" : "No");
printf(" P Parsimony method? %s\n",
(allwagner && !mixture) ? "Wagner" :
(!(allwagner || mixture)) ? "Camin-Sokal" : "(methods in mixture)");
printf(" F How often to report, in trees:%5ld\n",howoften);
printf(" H How many groups of%5ld trees:%6ld\n",howoften,howmanny);
printf(" O Outgroup root?");
if (outgropt)
printf(" Yes, at species number%3ld\n", outgrno);
else
printf(" No, use as outgroup species%3ld\n", outgrno);
printf(" S Branch and bound is simple? %s\n",
simple ? "Yes" : "No. reconsiders order of species");
printf(" T Use Threshold parsimony?");
if (thresh)
printf(" Yes, count steps up to%4.1f per char.\n", threshold);
else
printf(" No, use ordinary parsimony\n");
printf(" A Use ancestral states in input file? %s\n",
ancvar ? "Yes" : "No");
printf(" W Sites weighted? %s\n",
(weights ? "Yes" : "No"));
printf(" M Analyze multiple data sets?");
if (mulsets)
printf(" Yes, %2ld %s\n", msets,
(justwts ? "sets of weights" : "data sets"));
else
printf(" No\n");
printf(" 0 Terminal type (IBM PC, ANSI, none)? %s\n",
ibmpc ? "IBM PC" : ansi ? "ANSI" : "(none)");
printf(" 1 Print out the data at start of run %s\n",
printdata ? "Yes" : "No");
printf(" 2 Print indications of progress of run %s\n",
progress ? "Yes" : "No");
printf(" 3 Print out tree %s\n",
treeprint ? "Yes" : "No");
printf(" 4 Print out steps in each character %s\n",
stepbox ? "Yes" : "No");
printf(" 5 Print states at all nodes of tree %s\n",
ancseq ? "Yes" : "No");
printf(" 6 Write out trees onto tree file? %s\n",
trout ? "Yes" : "No");
if(weights && justwts) {
printf(
"WARNING: W option and Multiple Weights options are both on. ");
printf(
"The W menu option is unnecessary and has no additional effect. \n");
}
printf("\nAre these settings correct?");
printf(" (type Y or the letter for one to change)\n");
#ifdef WIN32
phyFillScreenColor();
#endif
scanf("%c%*[^\n]", &ch);
getchar();
uppercase(&ch);
if (ch == 'Y')
break;
if (strchr("WHFSOMPATX1234560",ch) != NULL) {
switch (ch) {
case 'X':
mixture = !mixture;
break;
case 'P':
allwagner = !allwagner;
break;
case 'A':
ancvar = !ancvar;
break;
case 'H':
inithowmany(&howmanny, howoften);
break;
case 'F':
inithowoften(&howoften);
break;
case 'S':
simple = !simple;
break;
case 'O':
outgropt = !outgropt;
if (outgropt)
initoutgroup(&outgrno, spp);
else outgrno = 1;
break;
case 'T':
thresh = !thresh;
if (thresh)
initthreshold(&threshold);
break;
case 'W':
weights = !weights;
break;
case 'M':
mulsets = !mulsets;
if (mulsets) {
printf("Multiple data sets or multiple weights?");
loopcount2 = 0;
do {
printf(" (type D or W)\n");
#ifdef WIN32
phyFillScreenColor();
#endif
scanf("%c%*[^\n]", &ch2);
getchar();
if (ch2 == '\n')
ch2 = ' ';
uppercase(&ch2);
countup(&loopcount2, 10);
} while ((ch2 != 'W') && (ch2 != 'D'));
justwts = (ch2 == 'W');
if (justwts)
justweights(&msets);
else
initdatasets(&msets);
}
break;
case '0':
initterminal(&ibmpc, &ansi);
break;
case '1':
printdata = !printdata;
break;
case '2':
progress = !progress;
break;
case '3':
treeprint = !treeprint;
break;
case '4':
stepbox = !stepbox;
break;
case '5':
ancseq = !ancseq;
break;
case '6':
trout = !trout;
break;
}
} else
printf("Not a possible option!\n");
countup(&loopcount, 100);
}
allsokal = (!allwagner && !mixture);
} /* getoptions */
void getoptions()
{
/* interactively set options */
long i;
long inseed0 = 0;
Char ch;
fprintf(outfile, "\nNeighbor-Joining/UPGMA method version %s\n\n",VERSION);
putchar('\n');
jumble = false;
lower = false;
outgrno = 1;
outgropt = false;
replicates = false;
trout = true;
upper = false;
printdata = false;
progress = true;
treeprint = true;
njoin = true;
for(;;) {
printf(ansi ? "\033[2J\033[H" : "\n");
printf("\nNeighbor-Joining/UPGMA method version %s\n\n",VERSION);
printf("Settings for this run:\n");
printf(" N Neighbor-joining or UPGMA tree? %s\n",
(njoin ? "Neighbor-joining" : "UPGMA"));
if (njoin) {
printf(" O Outgroup root?");
if (outgropt)
printf(" Yes, at species number%3ld\n", outgrno);
else
printf(" No, use as outgroup species%3ld\n", outgrno);
}
printf(" L Lower-triangular data matrix? %s\n",
(lower ? "Yes" : "No"));
printf(" R Upper-triangular data matrix? %s\n",
(upper ? "Yes" : "No"));
printf(" S Subreplicates? %s\n",
(replicates ? "Yes" : "No"));
printf(" J Randomize input order of species?");
if (jumble)
printf(" Yes (random number seed =%8ld)\n", inseed0);
else
printf(" No. Use input order\n");
printf(" M Analyze multiple data sets?");
if (mulsets)
printf(" Yes, %2ld sets\n", datasets);
else
printf(" No\n");
printf(" 0 Terminal type (IBM PC, ANSI, none)? %s\n",
(ibmpc ? "IBM PC" : ansi ? "ANSI" : "(none)"));
printf(" 1 Print out the data at start of run %s\n",
(printdata ? "Yes" : "No"));
printf(" 2 Print indications of progress of run %s\n",
(progress ? "Yes" : "No"));
printf(" 3 Print out tree %s\n",
(treeprint ? "Yes" : "No"));
printf(" 4 Write out trees onto tree file? %s\n",
(trout ? "Yes" : "No"));
printf("\n\n Y to accept these or type the letter for one to change\n");
#ifdef WIN32
phyFillScreenColor();
#endif
scanf("%c%*[^\n]", &ch);
getchar();
if (ch == '\n')
ch = ' ';
uppercase(&ch);
if (ch == 'Y')
break;
if (strchr("NJOULRSM01234",ch) != NULL){
switch (ch) {
case 'J':
jumble = !jumble;
if (jumble) {
do {
printf("Random number seed (must be odd)?\n");
#ifdef WIN32
phyFillScreenColor();
#endif
scanf("%ld%*[^\n]", &inseed);
getchar();
} while (!(inseed & 1));
inseed0 = inseed;
for (i = 0; i <= 5; i++)
seed[i] = 0;
i = 0;
do {
seed[i] = inseed & 63;
inseed /= 64;
i++;
} while (inseed != 0);
}
break;
case 'L':
lower = !lower;
break;
case 'O':
outgropt = !outgropt;
if (outgropt)
initoutgroup(&outgrno, spp);
else
outgrno = 1;
break;
case 'R':
upper = !upper;
break;
case 'S':
replicates = !replicates;
break;
case 'N':
njoin = !njoin;
break;
case 'M':
mulsets = !mulsets;
if (mulsets)
initdatasets(&datasets);
break;
case '0':
initterminal(&ibmpc, &ansi);
break;
case '1':
printdata = !printdata;
break;
case '2':
progress = !progress;
break;
case '3':
treeprint = !treeprint;
break;
case '4':
trout = !trout;
break;
}
} else
printf("Not a possible option!\n");
}
} /* getoptions */
void getoptions()
{
/* interactively set options */
Char ch;
putchar('\n');
sitelength = 6.0;
neili = false;
gama = false;
cvi = 0.0;
weights = false;
lower = false;
printdata = false;
progress = true;
restsites = true;
interleaved = true;
ttratio = 2.0;
for (;;) {
printf("%s", (ansi ? ("\033[2J\033[H") : "\n"));
printf("\nRestriction site or fragment distances, ");
printf("version %s\n\n",VERSION);
printf("Settings for this run:\n");
printf(" R Restriction sites or fragments? %s\n",
(restsites ? "Sites" : "Fragments"));
if (!restsites)
printf(" N Original or modified Nei/Li model? %s\n",
(neili ? "Original" : "Modified"));
if (restsites || !neili) {
printf(" G Gamma distribution of rates among sites?");
if (!gama)
printf(" No\n");
else
printf(" Yes\n");
printf(" T Transition/transversion ratio? %f\n", ttratio);
}
printf(" S Site length? %4.1f\n",sitelength);
printf(" L Form of distance matrix? %s\n",
(lower ? "Lower-triangular" : "Square"));
printf(" M Analyze multiple data sets?");
if (mulsets)
printf(" Yes, %2ld sets\n", datasets);
else
printf(" No\n");
printf(" I Input sequences interleaved? %s\n",
(interleaved ? "Yes" : "No, sequential"));
printf(" 0 Terminal type (IBM PC, ANSI, none)? %s\n",
ibmpc ? "IBM PC" : ansi ? "ANSI" : "(none)");
printf(" 1 Print out the data at start of run? %s\n",
(printdata ? "Yes" : "No"));
printf(" 2 Print indications of progress of run? %s\n",
(progress ? "Yes" : "No"));
printf("\n Y to accept these or type the letter for one to change\n");
#ifdef WIN32
phyFillScreenColor();
#endif
scanf("%c%*[^\n]", &ch);
getchar();
if (ch == '\n')
ch = ' ';
uppercase(&ch);
if (ch == 'Y')
break;
if (strchr("RDNGTSLMI012",ch) != NULL){
switch (ch) {
case 'R':
restsites = !restsites;
break;
case 'G':
if (restsites || !neili)
gama = !gama;
break;
case 'N':
if (!restsites)
neili = !neili;
break;
case 'T':
if (restsites || !neili)
initratio(&ttratio);
break;
case 'S':
do {
printf("New Sitelength?\n");
#ifdef WIN32
phyFillScreenColor();
#endif
scanf("%lf%*[^\n]", &sitelength);
getchar();
if (sitelength < 1.0)
printf("BAD RESTRICTION SITE LENGTH: %f\n", sitelength);
} while (sitelength < 1.0);
break;
case 'L':
lower = !lower;
break;
case 'M':
mulsets = !mulsets;
if (mulsets)
initdatasets(&datasets);
break;
case 'I':
interleaved = !interleaved;
break;
case '0':
initterminal(&ibmpc, &ansi);
break;
case '1':
printdata = !printdata;
break;
case '2':
progress = !progress;
break;
}
} else
printf("Not a possible option!\n");
}
if (gama) {
do {
printf(
"\nCoefficient of variation of substitution rate among sites (must be positive)?\n");
#ifdef WIN32
phyFillScreenColor();
#endif
scanf("%lf%*[^\n]", &cvi);
getchar();
} while (cvi <= 0.0);
cvi = 1.0 / (cvi * cvi);
printf("\n");
}
xi = (ttratio - 0.5)/(ttratio + 0.5);
xv = 1.0 - xi;
fracchange = xi*0.5 + xv*0.75;
} /* getoptions */