/*
* MrBayes 2.0
*
* John P. Huelsenbeck
* Department of Biology
* University of Rochester
* Rochester, NY 14627
*
* johnh@brahms.biology.rochester.edu
*
* Fredrik Ronquist
* Dept. Systematic Zoology
* Evolutionary Biology Centre
* Uppsala University
* Norbyv. 18D, SE-752 36 Uppsala, Sweden
*
* fredrik.ronquist@ebc.uu.se
*
*/
#include <stdio.h>
#include <stdlib.h>
#include <time.h>
#include <math.h>
#include <string.h>
#include "jph.h"
#include "tree.h"
#include "command.h"
#define VERSION_NUMBER 2.01
static void CommandLine (void);
static void InitializeMrBayes (void);
static void PrintHeader (void);
int nTaxa, nChar, *origDataMatrix, isNtaxaInitialized, isNcharInitialized, isMatrixAllocated,
dataType, *excludedSites, *sitePartitions, *charType, *charNStates, *calibrations, *constraints,
nConstraints, nCalibrations, *excludedTaxa, nGen, sampleFreq, printFreq, numChains,
isUserTreeDefined, isTreeRooted, enforceConstraints, enforceCalibrations, inferAncStates,
nRateCats, isPartitionDefined, nPartitions, outgroupNum, saveBrlens, burnIn, consensusType,
paramBurn, autoclose, nPerturbations, userBrlensDef, aaModelType, saveAncFiles, enforceCodonModel, aaCode,
inferPoseSel, lagNumber, inferRates, useCovarion, mcmcBurn, cycleFreq, calcPseudoBf, useParsCriterion;
long int randomSeed;
char *taxonLabels, subModel[20], baseFreqModel[20], ratesModel[20], clockModel[20],
tRatioModel[20], revRatesModel[20], nonRevRatesModel[20], partitionName[50],
shapeModel[20], siteRatesModel[20],constraintLabels[32][100], calibrationLabels[32][100],
outFile[100], qmatprModel[20], basefreqprModel[20],
brlenprModel[20], shapeprModel[20], siterateprModel[20], startingTreeModel[20],
defPartitionName[50], sumTreeFile[100], sumParmFile[100], codonModelType[20], omegaRatioModel[20],
omegaprModel[20], lagModel[20], lagprModel[20], covarionModelType[20], codingType[20], stateFreqPrModel[20];
double revRates[6], nonRevRates[12], shape, tRatio, siteRates[50],
calibrationTimes[32][2], chainTemp, qmatprExp, qmatprUni[2], basefreqprDir, brlenprExp,
brlenprUni[2], shapeprExp, shapeprUni[2], siterateprExp, siterateprUni[2], seqErrorProb,
speciationRate, extinctionRate, samplingFraction, omegaRatio, omegaprUni[2], omegaprExp,
lagprUni[2], lagprExp, qMatWinProp, piAlphaProp, rateWinProp, tuningProp, clockTuneProp, timeTuneProp, mTuneProp,
extendPProp, wormTuneProp, bdWinProp, omegaWinProp, rhoWinProp, omegaAlphaProp, invSlideProp,
switchWinProp, alphaWinProp, nodeTimeTuneProp, reconLimProp, tbrExtendPProp, tbrTuneProp, blTuneProp,
statefreqprDir, moveRates[100];
TreeNode *userTree, *userTreeRoot;
int main (void)
{
InitializeMrBayes ();
PrintHeader ();
SetUpCommandHierarchy ();
CommandLine ();
return (0);
}
void CommandLine (void)
{
int i;
char cmdStr[STRING_LENGTH];
for (;;)
{
printf ("MrBayes > ");
fflush (stdin);
fgets (cmdStr, STRING_LENGTH - 2, stdin);
i = 0;
while (cmdStr[i] != '\0' && cmdStr[i] != '\n')
i++;
cmdStr[i++] = ';';
cmdStr[i] = '\0';
printf ("\n");
if (cmdStr[0] != ';')
{
ParseCommand (cmdStr);
printf ("\n");
}
}
}
void InitializeMrBayes (void)
{
int i;
time_t curTime;
outgroupNum = 0;
strcpy (subModel, "1");
strcpy (baseFreqModel, "equal");
strcpy (ratesModel, "equal");
strcpy (clockModel, "unconstrained");
strcpy (tRatioModel, "estimate");
strcpy (revRatesModel, "estimate");
strcpy (nonRevRatesModel, "estimate");
strcpy (shapeModel, "estimate");
strcpy (partitionName, "none defined");
strcpy (siteRatesModel, "estimate");
strcpy (startingTreeModel, "random");
strcpy (qmatprModel, "uniform");
strcpy (basefreqprModel, "dirichlet");
strcpy (brlenprModel, "uniform");
strcpy (shapeprModel, "uniform");
strcpy (siterateprModel, "uniform");
strcpy (codingType, "all");
strcpy (stateFreqPrModel, "fixed");
qmatprUni[0] = 0.0000001;
qmatprUni[1] = 100.0;
basefreqprDir = 4.0;
statefreqprDir = 4.0;
brlenprUni[0] = 0.0000001;
brlenprUni[1] = 10.0;
shapeprUni[0] = 0.0000001;
shapeprUni[1] = 10.0;
siterateprUni[0] = 0.0000001;
siterateprUni[1] = 10.0;
isUserTreeDefined = NO;
nGen = 1000000;
sampleFreq = 100;
printFreq = 100;
numChains = 4;
chainTemp = 0.2;
strcpy (outFile, "mbout");
curTime = time(NULL);
randomSeed = (long int)curTime;
if (randomSeed < 0)
randomSeed = -randomSeed;
nConstraints = 0;
nCalibrations = 0;
enforceConstraints = NO;
enforceCalibrations = NO;
inferAncStates = NO;
shape = 0.5;
nRateCats = 4;
tRatio = 1.0;
for (i=0; i<6; i++)
revRates[i] = 1.0;
for (i=0; i<12; i++)
nonRevRates[i] = 1.0;
isPartitionDefined = NO;
nPartitions = 0;
for (i=0; i<50; i++)
siteRates[i] = 1.0;
saveBrlens = NO;
seqErrorProb = 0.0;
speciationRate = 1.0;
extinctionRate = 0.01;
samplingFraction = 1.0;
burnIn = 0;
consensusType = ALL_COMPAT;
strcpy (sumTreeFile, outFile);
strcat (sumTreeFile, ".t");
paramBurn = 0;
strcpy (sumParmFile, outFile);
strcat (sumParmFile, ".p.bp");
autoclose = NO;
nPerturbations = 0;
userBrlensDef = NO;
dataType = -1;
aaModelType = POISSON;
omegaRatio = 1.0;
saveAncFiles = NO;
enforceCodonModel = NO;
strcpy (covarionModelType, "ts98");
strcpy (codonModelType, "equal");
strcpy (omegaRatioModel, "estimate");
strcpy (omegaprModel, "uniform");
omegaprUni[0] = 0.0;
omegaprUni[1] = 50.0;
omegaprExp = 1.0;
inferPoseSel = NO;
lagNumber = 1;
strcpy (lagModel, "user defined");
strcpy (lagprModel, "fixed");
lagprUni[0] = 0.0;
lagprUni[1] = 20.0;
lagprExp = 1.0;
inferRates = NO;
useCovarion = NO;
mcmcBurn = 0;
cycleFreq = 1000;
calcPseudoBf = NO;
useParsCriterion = NO;
qMatWinProp = 2.0;
piAlphaProp = 500.0;
rateWinProp = 1.0;
tuningProp = 2.0 * log(1.1);
clockTuneProp = 2.0 * log(1.1);
timeTuneProp = 2.0 * log(1.1);
mTuneProp = 0.5 * log(1.1);
extendPProp = 0.8;
wormTuneProp = 2.0 * log(1.1);
bdWinProp = 1.0;
omegaWinProp = 1.0;
rhoWinProp = 0.2;
omegaAlphaProp = 50.0;
invSlideProp = 0.1;
switchWinProp = 1.0;
alphaWinProp = 0.1;
nodeTimeTuneProp = 2.0 * log(1.1);
reconLimProp = 5.0;
tbrExtendPProp = 0.8;
tbrTuneProp = 2.0 * log(1.1);
blTuneProp = 10.0 * 2.0 * log(1.1);
moveRates[ 0] = 1.0; /* CHANGE_QMAT */
moveRates[ 1] = 1.0; /* CHANGE_BASEFREQS */
moveRates[ 2] = 1.0; /* CHANGE_GAMMA_SHAPE */
moveRates[ 3] = 1.0; /* CHANGE_SITE_RATES */
moveRates[ 4] = 40.0; /* CHANGE_UNROOT_LOCAL */
moveRates[ 5] = 25.0; /* CHANGE_CLOCK_LOCAL */
moveRates[ 6] = 25.0; /* CHANGE_CLOCK_TIME_LOCAL */
moveRates[ 7] = 10.0; /* CHANGE_TREE_HEIGHT */
moveRates[ 8] = 2.0; /* CHANGE_WORM */
moveRates[ 9] = 10.0; /* CHANGE_NODE_TIME */
moveRates[10] = 1.0; /* CHANGE_BD_PARAMS */
moveRates[11] = 1.0; /* CHANGE_OMEGA */
moveRates[12] = 1.0; /* CHANGE_OMEGA_PROBS */
moveRates[13] = 1.0; /* CHANGE_AUTO_CORR */
moveRates[14] = 1.0; /* CHANGE_LAG */
moveRates[15] = 0.0; /* CHANGE_TREE_SPR */
moveRates[16] = 1.0; /* CHANGE_INV_P */
moveRates[17] = 1.0; /* CHANGE_SWITCH_RATE */
moveRates[18] = 0.0; /* CHANGE_UNROOT_TBR */
moveRates[19] = 1.0; /* CHANGE_GCSWITCH */
moveRates[20] = 0.0; /* CHANGE_TREE_FTBR */
moveRates[21] = 0.0; /* CHANGE_BRLEN */
moveRates[22] = 0.0; /* CHANGE_ERASER */
moveRates[23] = 0.0; /* CHANGE_TREE_SPR2 */
moveRates[24] = 0.0; /* CHANGE_TREE_TBR2 */
moveRates[25] = 1.0; /* CHANGE_BETA_SHAPE */
}
void PrintHeader (void)
{
printf ("\n\n");
printf (" MrBayes %1.2lf\n\n", VERSION_NUMBER);
printf (" (Bayesian Analysis of Phylogeny)\n\n");
printf (" by\n\n");
printf (" John P. Huelsenbeck (1) and Fredrik Ronquist (2)\n\n");
printf (" (1) Department of Biology\n");
printf (" University of Rochester\n");
printf (" johnh@brahms.biology.rochester.edu\n\n");
printf (" (2) Department of Systematic Zoology\n");
printf (" Evolutionary Biology Centre\n");
printf (" Uppsala University\n");
printf (" fredrik.ronquist@ebc.uu.se\n\n");
printf (" Type \"help\" or \"help <command>\" for information\n");
printf (" on the commands that are available.\n\n\n");
}
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