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bayes.c
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/*
* MrBayes 3
*
* (c) 2002-2023
*
* John P. Huelsenbeck
* Dept. Integrative Biology
* University of California, Berkeley
* Berkeley, CA 94720-3140
*
* Fredrik Ronquist
* Swedish Museum of Natural History
* Box 50007
* SE-10405 Stockholm, SWEDEN
*
* With important contributions by
*
* Paul van der Mark ([email protected])
* Maxim Teslenko ([email protected])
* Chi Zhang ([email protected])
*
* and by many users (run 'acknowledgments' to see more info)
*
* This program is free software; you can redistribute it and/or
* modify it 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 (www.gnu.org).
*
*/
#include "bayes.h"
#include "command.h"
#include "model.h"
#include "sumpt.h"
#include "utils.h"
/* We only do proper command line parsing if we're on a system where the
unistd.h header is available */
#ifdef HAVE_UNISTD_H
#define UNIX_COMMAND_LINE_PARSING 1
#include <unistd.h> /* getopt() */
#endif
#ifdef HAVE_LIBREADLINE
# if defined(HAVE_READLINE_READLINE_H)
# include <readline/readline.h>
# elif defined(HAVE_READLINE_H)
# include <readline.h>
# else
# /* Library available, but header files are not. */
# /* This typically happens on Linux where libraries may be split
# into runtime and development packages. See Github Issue #182. */
# undef HAVE_LIBREADLINE
# undef HAVE_READLINE_HISTORY
# endif
# endif /* HAVE_LIBREADLINE */
#ifdef HAVE_READLINE_HISTORY
# if defined(HAVE_READLINE_HISTORY_H)
# include <readline/history.h>
# elif defined(HAVE_HISTORY_H)
# include <history.h>
# else
# undef HAVE_READLINE_HISTORY
# endif
#endif /* HAVE_READLINE_HISTORY */
#ifdef HAVE_LIBREADLINE
static char **readline_completion(const char *, int, int);
#endif
/* local prototypes */
int CommandLine (int argc, char **argv);
void GetTimeSeed (void);
int InitializeMrBayes (void);
void PrintHeader (void);
int ReinitializeMrBayes (void);
/* global variables, declared in this file */
BitsLong bitsLongWithAllBitsSet; /* BitsLong with all bits set, for bit ops */
ModelParams defaultModel; /* Default model; vals set in InitializeMrBayes */
int defTaxa; /* flag for whether number of taxa is known */
int defChars; /* flag for whether number of chars is known */
int defMatrix; /* flag for whether matrix is successful read */
int defPartition; /* flag for whether character partition is read */
int defPairs; /* flag for whether pairs are read */
Doublet doublet[16]; /* holds information on states for doublets */
int fileNameChanged; /* has file name been changed ? */
RandLong globalSeed; /* seed that is initialized at start up */
char **modelIndicatorParams; /* model indicator params */
char ***modelElementNames; /* names for component models */
int nBitsInALong; /* number of bits in a BitsLong */
int nPThreads; /* number of pthreads to use */
int numUserTrees; /* number of defined user trees */
int readComment; /* should we read comment (looking for &) ? */
int readWord; /* should we read word next ? */
RandLong runIDSeed; /* seed used only for determining run ID [stamp] */
RandLong swapSeed; /* seed used only for determining which to swap */
int userLevel; /* user level */
PolyTree *userTree[MAX_NUM_USERTREES];/* array of user trees */
char workingDir[100]; /* working directory */
#if defined (MPI_ENABLED)
int proc_id; /* process ID (0, 1, ..., num_procs-1) */
int num_procs; /* number of active processors */
MrBFlt myStateInfo[7]; /* likelihood/prior/heat/ran/moveInfo vals of me */
MrBFlt partnerStateInfo[7]; /* likelihood/prior/heat/ran/moveInfo vals of partner */
#endif
int main (int argc, char *argv[])
{
int i;
# if defined (MPI_ENABLED)
int ierror;
# endif
# if defined (WIN_VERSION)
HANDLE scbh;
BOOL ok;
DWORD lastError;
COORD largestWindow;
CONSOLE_SCREEN_BUFFER_INFO csbi;
int currBottom;
char poltmp[256];
scbh = GetStdHandle(STD_OUTPUT_HANDLE);
GetConsoleScreenBufferInfo(scbh, &csbi);
currBottom = csbi.srWindow.Bottom;
largestWindow = GetLargestConsoleWindowSize(scbh);
/* Allow for screen buffer 3000 lines long and 140 characters wide */
csbi.dwSize.Y = 3000;
csbi.dwSize.X = 140;
SetConsoleScreenBufferSize(scbh, csbi.dwSize);
/* Allow for maximum possible screen height */
csbi.srWindow.Left = 0; /* no change relative to current value */
csbi.srWindow.Top = 0; /* no change relative to current value */
csbi.srWindow.Right = 0; /* no change relative to current value */
csbi.srWindow.Bottom = largestWindow.Y - currBottom -10; /**/
ok = SetConsoleWindowInfo(scbh, FALSE, &csbi.srWindow);
if (ok == FALSE)
{
lastError = GetLastError();
GetConsoleScreenBufferInfo(scbh, &csbi);
sprintf(poltmp, "\nlastError = %ld", lastError);
// printf (poltmp);
}
# endif
/* calculate the size of a long - used by bit manipulation functions */
nBitsInALong = sizeof(BitsLong) * 8;
for (i=0; i<nBitsInALong; i++)
SetBit(i, &bitsLongWithAllBitsSet);
# if defined (__MWERKS__) & defined (MAC_VERSION)
/* Set up interface when using the Metrowerks compiler. This
should work for either Macintosh or Windows. */
SIOUXSetTitle("\pMrBayes v3.2.7");
SIOUXSettings.fontface = 0; /* plain=0; bold=1 */
SIOUXSettings.setupmenus = 0;
SIOUXSettings.autocloseonquit = 1;
SIOUXSettings.asktosaveonclose = 0;
SIOUXSettings.rows = 60;
SIOUXSettings.columns = 90;
# endif
# if defined (MPI_ENABLED)
ierror = MPI_Init(&argc, &argv);
if (ierror != MPI_SUCCESS)
{
MrBayesPrint ("%s Problem initializing MPI\n", spacer);
exit (1);
}
ierror = MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
if (ierror != MPI_SUCCESS)
{
MrBayesPrint ("%s Problem getting the number of processors\n", spacer);
exit (1);
}
ierror = MPI_Comm_rank(MPI_COMM_WORLD, &proc_id);
if (ierror != MPI_SUCCESS)
{
MrBayesPrint ("%s Problem getting processors rank\n", spacer);
exit (1);
}
# endif
# ifdef HAVE_LIBREADLINE
rl_attempted_completion_function = readline_completion;
# ifdef HAVE_READLINE_HISTORY
using_history();
# endif /* HAVE_READLINE_HISTORY */
# endif /* HAVE_LIBREADLINE */
/* Set up parameter table. */
SetUpParms ();
/* initialize seed using current time */
GetTimeSeed ();
/* Initialize the variables of the program. */
InitializeMrBayes ();
/* Go to the command line, process any arguments passed to the program
and then wait for input. */
i = CommandLine (argc, argv);
# if defined (MPI_ENABLED)
MPI_Finalize();
# endif
if (i == ERROR)
return (1);
else
return (0);
}
int CommandLine (int argc, char **argv)
{
int i, message, nProcessedArgs;
char cmdStr[CMD_STRING_LENGTH];
# ifdef HAVE_LIBREADLINE
# ifndef MPI_ENABLED
char *cmdStrP;
# endif
# endif
# if defined (MPI_ENABLED)
int ierror;
# endif
for (i = 0; i < CMD_STRING_LENGTH; i++) cmdStr[i] = '\0';
#ifdef UNIX_COMMAND_LINE_PARSING
{
int ch; /* the option character */
int interactive = 0; /* enable/disable interactive mode */
/* Do command line parsing on Unix-like systems */
while ((ch = getopt(argc, argv, "hiIv")) != -1) {
switch (ch) {
case 'h': /* help */
/* Display (very short) command synopsis and terminate
* succesfully */
puts("MrBayes, Bayesian Analysis of Phylogeny\n");
puts("Usage:");
printf("\t%s [-i] [filename ...]\n", argv[0]);
printf("\t%s -v\n", argv[0]);
printf("\t%s -h\n", argv[0]);
putchar('\n');
puts("Options:");
puts("\t-i\tForce interactive mode");
puts("\t\tNon-interactive mode is the default when a "
"filename is given");
puts("\t\tInteractive mode is the default when no filename is "
"given");
puts("\t-v\tDisplay version information and exit");
puts("\t-h\tDisplay this short help text and exit");
return NO_ERROR;
break; /* NOTREACHED */
case 'i': /* interactive */
case 'I': /* interactive */
/* Force enable interactive mode */
interactive = 1;
break;
case 'v': /* version */
/* Display the same information that is displayed by the
* "Version" interactive command and terminate successfully */
puts("MrBayes, Bayesian Analysis of Phylogeny\n");
printf("Version: %s\n", VERSION_NUMBER);
fputs("Features: ", stdout);
#ifdef SSE_ENABLED
fputs(" SSE", stdout);
#endif
#ifdef AVX_ENABLED
fputs(" AVX", stdout);
#endif
#ifdef FMA_ENABLED
fputs(" FMA", stdout);
#endif
#ifdef BEAGLE_ENABLED
fputs(" Beagle", stdout);
#endif
#ifdef MPI_ENABLED
fputs(" MPI", stdout);
#endif
#ifdef HAVE_LIBREADLINE
fputs(" readline", stdout);
#endif
putchar('\n');
#if defined(HOST_TYPE) && defined(HOST_CPU)
printf("Host type: %s (CPU: %s)\n", HOST_TYPE, HOST_CPU);
#endif
#if defined(COMPILER_VENDOR) && defined(COMPILER_VERSION)
printf(
"Compiler: %s %s\n", COMPILER_VENDOR, COMPILER_VERSION);
#endif
return NO_ERROR;
break; /* NOTREACHED */
case '?': /* unknown */
default: /* unknown */
fprintf(stderr,
"Error in command line parsing (see '%s -h')\n", argv[0]);
return ERROR;
}
}
if (optind == argc) {
/* If no further operands are available (i.e. there are no files to
* process), switch to interactive mode */
interactive = 1;
}
if (interactive) {
mode = INTERACTIVE;
autoClose = NO;
autoOverwrite = YES;
noWarn = NO;
quitOnError = NO;
} else {
mode = NONINTERACTIVE;
autoClose = YES;
autoOverwrite = YES;
noWarn = YES;
quitOnError = YES;
}
nProcessedArgs = optind;
}
#else /* !UNIX_COMMAND_LINE_PARSING */
/* wait for user-input commands */
nProcessedArgs = 1; /* first argument is program name and needs not be processed */
if (nProcessedArgs < argc)
{
mode = NONINTERACTIVE; /* when a command is passed into the program, the default is to exit without listening to stdin */
autoClose = YES;
autoOverwrite = YES;
noWarn = YES;
quitOnError = YES;
}
#endif
/* Display MrBayes header *after* parsing the command line un Unix systems */
PrintHeader();
for (;;)
{
if (nProcessedArgs < argc)
{
#ifndef UNIX_COMMAND_LINE_PARSING
/* we are here only if a command that has been passed
into the program remains to be processed */
if (nProcessedArgs == 1 && (strcmp(argv[1],"-i") == 0 || strcmp(argv[1],"-I") == 0))
{
mode = INTERACTIVE;
autoClose = NO;
autoOverwrite = YES;
noWarn = NO;
quitOnError = NO;
}
else
#endif
sprintf (cmdStr, "Execute %s", argv[nProcessedArgs]);
nProcessedArgs++;
}
else
{
/* first check if we are in noninteractive mode and quit if so */
if (mode == NONINTERACTIVE)
{
MrBayesPrint ("%s Tasks completed, exiting program because mode is noninteractive\n", spacer);
MrBayesPrint ("%s To return control to the command line after completion of file processing, \n", spacer);
MrBayesPrint ("%s set mode to interactive with 'mb -i <filename>' (i is for interactive)\n", spacer);
MrBayesPrint ("%s or use 'set mode=interactive'\n\n", spacer);
return (NO_ERROR);
}
/* normally, we simply wait at the prompt for a
user action */
# if defined (MPI_ENABLED)
if (proc_id == 0)
{
/* do not use readline because OpenMPI does not handle it */
MrBayesPrint ("MrBayes > ");
fflush (stdin);
if (fgets (cmdStr, CMD_STRING_LENGTH - 2, stdin) == NULL)
{
if (feof(stdin))
MrBayesPrint ("%s End of File encountered on stdin; quitting\n", spacer);
else
MrBayesPrint ("%s Could not read command from stdin; quitting\n", spacer);
strcpy (cmdStr,"quit;\n");
}
}
ierror = MPI_Bcast (&cmdStr, CMD_STRING_LENGTH, MPI_CHAR, 0, MPI_COMM_WORLD);
if (ierror != MPI_SUCCESS)
{
MrBayesPrint ("%s Problem broadcasting command string\n", spacer);
}
# else
# ifdef HAVE_LIBREADLINE
cmdStrP = readline("MrBayes > ");
if (cmdStrP!=NULL)
{
strncpy (cmdStr, cmdStrP, CMD_STRING_LENGTH - 2);
# ifdef HAVE_READLINE_HISTORY
if (*cmdStrP)
add_history (cmdStrP);
# endif /* HAVE_READLINE_HISTORY */
free (cmdStrP);
}
else /* fall through to if (feof(stdin))..*/
# else
MrBayesPrint ("MrBayes > ");
fflush (stdin);
if (fgets (cmdStr, CMD_STRING_LENGTH - 2, stdin) == NULL)
# endif
{
if (feof(stdin))
MrBayesPrint ("%s End of File encountered on stdin; quitting\n", spacer);
else
MrBayesPrint ("%s Could not read command from stdin; quitting\n", spacer);
strcpy (cmdStr,"quit;\n");
}
# endif
}
i = 0;
while (cmdStr[i] != '\0' && cmdStr[i] != '\n')
i++;
cmdStr[i++] = ';';
cmdStr[i] = '\0';
MrBayesPrint ("\n");
if (cmdStr[0] != ';')
{
/* check that all characters in the string are valid */
if (CheckStringValidity (cmdStr) == ERROR)
{
MrBayesPrint (" Unknown character in command string\n\n");
}
else
{
expecting = Expecting(COMMAND);
message = ParseCommand (cmdStr);
if (message == NO_ERROR_QUIT)
return (NO_ERROR);
if (message == ERROR && quitOnError == YES)
{
MrBayesPrint ("%s Will exit with signal 1 (error) because quitonerror is set to yes\n", spacer);
MrBayesPrint ("%s If you want control to be returned to the command line on error,\n", spacer);
MrBayesPrint ("%s use 'mb -i <filename>' (i is for interactive) or use 'set quitonerror=no'\n\n", spacer);
return (ERROR);
}
# if defined (MPI_ENABLED)
ierror = MPI_Barrier (MPI_COMM_WORLD);
if (ierror != MPI_SUCCESS)
{
MrBayesPrint ("%s Problem at command barrier\n", spacer);
}
# endif
MrBayesPrint ("\n");
}
}
}
}
#ifdef HAVE_LIBREADLINE
extern char *command_generator(const char *text, int state);
char **readline_completion (const char *text, int start, int stop)
{
char **matches = (char **) NULL;
# ifdef COMPLETIONMATCHES
if (start == 0)
matches = rl_completion_matches (text, command_generator);
# endif
return (matches);
}
#endif
void GetTimeSeed (void)
{
time_t curTime;
# if defined (MPI_ENABLED)
int ierror;
if (proc_id == 0)
{
curTime = time(NULL);
globalSeed = (RandLong)curTime;
if (globalSeed < 0)
globalSeed = -globalSeed;
}
ierror = MPI_Bcast(&globalSeed, 1, MPI_LONG, 0, MPI_COMM_WORLD);
if (ierror != MPI_SUCCESS)
{
MrBayesPrint ("%s Problem broadcasting seed\n", spacer);
}
if (proc_id == 0)
{
/* Note: swapSeed will often be same as globalSeed */
curTime = time(NULL);
swapSeed = (RandLong)curTime;
if (swapSeed < 0)
swapSeed = -swapSeed;
}
ierror = MPI_Bcast(&swapSeed, 1, MPI_LONG, 0, MPI_COMM_WORLD);
if (ierror != MPI_SUCCESS)
{
MrBayesPrint ("%s Problem broadcasting swap seed\n", spacer);
}
if (proc_id == 0)
{
/* Note: runIDSeed will often be same as globalSeed */
curTime = time(NULL);
runIDSeed = (RandLong)curTime;
if (runIDSeed < 0)
runIDSeed = -runIDSeed;
}
ierror = MPI_Bcast(&runIDSeed, 1, MPI_LONG, 0, MPI_COMM_WORLD);
if (ierror != MPI_SUCCESS)
{
MrBayesPrint ("%s Problem broadcasting run ID seed\n", spacer);
}
# else
curTime = time(NULL);
globalSeed = (RandLong)curTime;
if (globalSeed < 0)
globalSeed = -globalSeed;
/* Note: swapSeed will often be the same as globalSeed */
curTime = time(NULL);
swapSeed = (RandLong)curTime;
if (swapSeed < 0)
swapSeed = -swapSeed;
/* Note: runIDSeed will often be the same as globalSeed */
curTime = time(NULL);
runIDSeed = (RandLong)curTime;
if (runIDSeed < 0)
runIDSeed = -runIDSeed;
# endif
}
int InitializeMrBayes (void)
{
/* this function initializes the program; only call it at the start of execution */
int i, j, growthFxn[6];
nBitsInALong = sizeof(BitsLong) * 8; /* global variable: number of bits in a BitsLong */
userLevel = STANDARD_USER; /* default user level */
readWord = NO; /* should we read a word next ? */
readComment = NO; /* should we read comments? (used by tree cmd) */
fileNameChanged = NO; /* file name changed ? (used by a few commands) */
echoMB = YES; /* flag used by Manual to control printing */
# if defined (MPI_ENABLED)
sprintf (manFileName, "commref_mb%sp.txt", VERSION_NUMBER); /* name of command reference file */
# else
sprintf (manFileName, "commref_mb%s.txt", VERSION_NUMBER); /* name of command reference file */
# endif
for (i=0; i<NUM_ALLOCS; i++) /* set allocated memory to NO */
memAllocs[i] = NO;
logToFile = NO; /* should screen output be logged to a file */
strcpy(logFileName, "log.out"); /* name of the log file */
logFileFp = NULL; /* file pointer to log file */
replaceLogFile = YES; /* should logfile be replace/appended to */
autoClose = NO; /* set default autoclose */
autoOverwrite = YES; /* set default autoOverwrite */
noWarn = NO; /* set default */
quitOnError = NO; /* set default quitOnError */
inferAncStates = NO; /* set default inferAncStates */
inferSiteOmegas = NO; /* set default inferSiteOmegas */
inferSiteRates = NO; /* set default inferSiteRates */
inferPosSel = NO; /* set default inferPosSel */
inComment = NO; /* not in comment */
numComments = 0; /* no comments encountered yet */
mode = INTERACTIVE; /* set default mode */
numOpenExeFiles = 0; /* no execute files open yet */
scientific = YES; /* print to file using scientific format? */
precision = 6; /* set default precision */
showmovesParams.allavailable = NO; /* do not show all available moves */
strcpy(workingDir,""); /* working directory */
# if defined (BEAGLE_ENABLED)
# if defined (WIN_VERSION)
tryToUseBEAGLE = NO; /* try to use the BEAGLE library (NO until SSE code works in Win) */
# else
/* Try using Beagle */
/*
* Note: The old (2015) comment from Chi says that there is some issue with
* single precision SSE code. This issue is unknown to us at this point
* in time (2019, four years later).
*
* */
tryToUseBEAGLE = YES; /* try to use the BEAGLE library if not Win (NO until SSE single prec. works) */
# endif
beagleScalingScheme = MB_BEAGLE_SCALE_DYNAMIC; /* use BEAGLE dynamic scaling */
beagleFlags = BEAGLE_FLAG_PROCESSOR_CPU; /* default to generic CPU */
beagleResourceNumber = 99; /* default to auto-resource selection */
// SSE instructions do not work in Windows environment
// beagleFlags |= BEAGLE_FLAG_VECTOR_SSE; /* default to SSE code */
beagleResource = NULL;
beagleResourceCount = 0; /* default has no list */
beagleInstanceCount = 0; /* no BEAGLE instances */
beagleScalingFrequency = 1000;
beagleFlags &= ~BEAGLE_FLAG_PRECISION_DOUBLE; /* Use Beagle in single precision mode */
beagleFlags |= BEAGLE_FLAG_PRECISION_SINGLE;
# if defined (BEAGLE_V3_ENABLED)
beagleFlags |= BEAGLE_FLAG_THREADING_CPP; /* default to use threads on CPU */
beagleThreadCount = 99; /* default to auto threading */
beagleAllFloatTips = NO; /* default to using compact tips */
# endif
# endif
/* set the proposal information */
SetUpMoveTypes ();
/* Set up rates for standard amino acid models, in case we need them. */
if (SetAARates () == ERROR)
return (ERROR);
/* set up doublet information */
doublet[ 0].first = 1; doublet[ 0].second = 1;
doublet[ 1].first = 1; doublet[ 1].second = 2;
doublet[ 2].first = 1; doublet[ 2].second = 4;
doublet[ 3].first = 1; doublet[ 3].second = 8;
doublet[ 4].first = 2; doublet[ 4].second = 1;
doublet[ 5].first = 2; doublet[ 5].second = 2;
doublet[ 6].first = 2; doublet[ 6].second = 4;
doublet[ 7].first = 2; doublet[ 7].second = 8;
doublet[ 8].first = 4; doublet[ 8].second = 1;
doublet[ 9].first = 4; doublet[ 9].second = 2;
doublet[10].first = 4; doublet[10].second = 4;
doublet[11].first = 4; doublet[11].second = 8;
doublet[12].first = 8; doublet[12].second = 1;
doublet[13].first = 8; doublet[13].second = 2;
doublet[14].first = 8; doublet[14].second = 4;
doublet[15].first = 8; doublet[15].second = 8;
/* user trees */
for (i=0; i<MAX_NUM_USERTREES; i++)
userTree[i] = NULL;
/* parameter values */
paramValues = NULL;
intValues = NULL;
/* Prior model settings */
defaultModel.dataType = DNA; /* datatype */
defaultModel.coding = 0; /* ascertainment bias */
strcpy(defaultModel.codingString, "All"); /* ascertainment bias string */
strcpy(defaultModel.nucModel, "4by4"); /* nucleotide model */
strcpy(defaultModel.nst, "1"); /* number of substitution types */
strcpy(defaultModel.aaModelPr, "Fixed"); /* amino acid model prior */
for (i=0; i<10; i++)
defaultModel.aaModelPrProbs[i] = 0.0;
strcpy(defaultModel.aaModel, "Poisson"); /* amino acid model */
strcpy(defaultModel.parsModel, "No"); /* do not use parsimony model */
strcpy(defaultModel.statefreqModel, "Stationary"); /* use stationary model */ //SK
strcpy(defaultModel.geneticCode, "Universal"); /* genetic code */
strcpy(defaultModel.ploidy, "Diploid"); /* ploidy level */
strcpy(defaultModel.omegaVar, "Equal"); /* omega variation */
strcpy(defaultModel.ratesModel, "Equal"); /* rates across sites model */
defaultModel.numGammaCats = 4; /* number of categories for gamma approximation */
defaultModel.numLnormCats = 4; /* number of categories for lnorm approximation */
defaultModel.numMixtCats = 4; /* number of components in rate mixture */
strcpy(defaultModel.useGibbs,"No"); /* do not use Gibbs sampling of rate cats by default */
defaultModel.gibbsFreq = 100; /* default Gibbs sampling frequency of rate cats*/
defaultModel.numBetaCats = 5; /* number of categories for beta approximation */
strcpy(defaultModel.covarionModel, "No"); /* use covarion model? (yes/no) */
strcpy(defaultModel.augmentData, "No"); /* should data be augmented */
strcpy(defaultModel.tRatioPr, "Beta"); /* prior for ti/tv rate ratio */
defaultModel.tRatioFix = 1.0;
defaultModel.tRatioDir[0] = 1.0;
defaultModel.tRatioDir[1] = 1.0;
strcpy(defaultModel.revMatPr, "Dirichlet"); /* prior for GTR model (nucleotides) */
for (i=0; i<6; i++)
{
defaultModel.revMatFix[i] = 1.0;
defaultModel.revMatDir[i] = 1.0;
}
defaultModel.revMatSymDir = 1.0; /* default prior for GTR mixed model */
strcpy (defaultModel.aaRevMatPr, "Dirichlet"); /* prior for GTR model (proteins) */
/* Prior for state frequencies at the root. Not really necessary,
* as statefreqModel is set to "Stationary" by default" */ //SK
strcpy(defaultModel.rootFreqPr, "Dirichlet"); /* prior for root freq (not really necessary) */
for (i=0; i<190; i++)
{
defaultModel.aaRevMatFix[i] = 1.0;
defaultModel.aaRevMatDir[i] = 1.0;
}
strcpy(defaultModel.omegaPr, "Dirichlet"); /* prior for omega */
defaultModel.omegaFix = 1.0;
defaultModel.omegaDir[0] = 1.0;
defaultModel.omegaDir[1] = 1.0;
strcpy(defaultModel.ny98omega1pr, "Beta"); /* prior for class 1 omega (Ny98 model) */
defaultModel.ny98omega1Fixed = 0.1;
defaultModel.ny98omega1Beta[0] = 1.0;
defaultModel.ny98omega1Beta[1] = 1.0;
strcpy(defaultModel.ny98omega3pr, "Exponential"); /* prior for class 3 omega (Ny98 model) */
defaultModel.ny98omega3Fixed = 2.0;
defaultModel.ny98omega3Uni[0] = 1.0;
defaultModel.ny98omega3Uni[1] = 50.0;
defaultModel.ny98omega3Exp = 1.0;
strcpy(defaultModel.m3omegapr, "Exponential"); /* prior for all three omegas (M3 model) */
defaultModel.m3omegaFixed[0] = 0.1;
defaultModel.m3omegaFixed[1] = 1.0;
defaultModel.m3omegaFixed[2] = 2.0;
strcpy(defaultModel.m10betapr, "Uniform"); /* prior for omega variation (M10 model) */
strcpy(defaultModel.m10gammapr, "Uniform");
defaultModel.m10betaUni[0] = 0.0;
defaultModel.m10betaUni[1] = 20.0;
defaultModel.m10betaExp = 1.0;
defaultModel.m10betaFix[0] = 1.0;
defaultModel.m10betaFix[1] = 1.0;
defaultModel.m10gammaUni[0] = 0.0;
defaultModel.m10gammaUni[1] = 20.0;
defaultModel.m10gammaExp = 1.0;
defaultModel.m10gammaFix[0] = 1.0;
defaultModel.m10gammaFix[1] = 1.0;
defaultModel.numM10GammaCats = 4;
defaultModel.numM10BetaCats = 4;
strcpy(defaultModel.codonCatFreqPr, "Dirichlet"); /* prior for selection cat frequencies */
defaultModel.codonCatFreqFix[0] = 1.0/3.0;
defaultModel.codonCatFreqFix[1] = 1.0/3.0;
defaultModel.codonCatFreqFix[2] = 1.0/3.0;
defaultModel.codonCatDir[0] = 1.0;
defaultModel.codonCatDir[1] = 1.0;
defaultModel.codonCatDir[2] = 1.0;
strcpy(defaultModel.stateFreqPr, "Dirichlet"); /* prior for character state frequencies */
strcpy(defaultModel.stateFreqsFixType, "Equal");
for (i=0; i<200; i++)
{
defaultModel.stateFreqsFix[i] = 0.0;
defaultModel.stateFreqsDir[i] = 1.0;
}
defaultModel.numDirParams = 0;
strcpy(defaultModel.shapePr, "Exponential"); /* prior for gamma/lnorm shape parameter */
defaultModel.shapeFix = 0.5;
defaultModel.shapeUni[0] = MIN_SHAPE_PARAM;
defaultModel.shapeUni[1] = MAX_SHAPE_PARAM;
defaultModel.shapeExp = 1.0;
strcpy(defaultModel.pInvarPr, "Uniform"); /* prior for proportion of invariable sites */
defaultModel.pInvarFix = 0.1;
defaultModel.pInvarUni[0] = 0.0;
defaultModel.pInvarUni[1] = 1.0;
strcpy(defaultModel.adGammaCorPr, "Uniform"); /* prior for correlation param of adGamma model */
defaultModel.adgCorrFix = 0.0;
defaultModel.adgCorrUni[0] = -1.0;
defaultModel.adgCorrUni[1] = 1.0;
strcpy(defaultModel.covSwitchPr, "Uniform"); /* prior for switching rates of covarion model */
defaultModel.covswitchFix[0] = 1.0;
defaultModel.covswitchFix[1] = 1.0;
defaultModel.covswitchUni[0] = 0.0;
defaultModel.covswitchUni[1] = 100.0;
defaultModel.covswitchExp = 1.0;
strcpy(defaultModel.symPiPr, "Fixed"); /* prior for pi when unidentifiable states used */
defaultModel.symBetaFix = -1.0;
defaultModel.symBetaUni[0] = 0.0;
defaultModel.symBetaUni[1] = 20.0;
defaultModel.symBetaExp = 2;
strcpy(defaultModel.brownCorrPr, "Fixed"); /* prior on correlation of brownian model */
defaultModel.brownCorrFix = 0.0;
defaultModel.brownCorrUni[0] = -1.0;
defaultModel.brownCorrUni[1] = 1.0;
strcpy(defaultModel.brownScalePr, "Gamma"); /* prior on scales of brownian model */
defaultModel.brownScaleFix = 10.0;
defaultModel.brownScaleUni[0] = 0.0;
defaultModel.brownScaleUni[1] = 100.0;
defaultModel.brownScaleGamma[0] = 1.0;
defaultModel.brownScaleGamma[1] = 10.0;
strcpy(defaultModel.topologyPr, "Uniform"); /* prior for tree topology */
defaultModel.topologyFix = -1; /* user tree index to use for fixed topology */
defaultModel.activeConstraints = NULL; /* which constraints are active */
strcpy(defaultModel.brlensPr, "Unconstrained"); /* prior on branch lengths */
defaultModel.brlensFix = -1; /* user tree index to use for fixed brlens */
defaultModel.brlensUni[0] = BRLENS_MIN;
defaultModel.brlensUni[1] = 10.0;
defaultModel.brlensExp = 10.0;
defaultModel.brlens2Exp[0]= 100.0; /* 1st param of twoExp prior (for internal branches) */
defaultModel.brlens2Exp[1]= 10.0; /* 2nd param of twoExp prior (for external branches) */
defaultModel.brlensDir[0] = 1.0; /* 1st param of GammaDir prior */
// defaultModel.brlensDir[0] = 3.0; /* 1st param of invGamDir prior */
defaultModel.brlensDir[1] = 0.1; /* 2nd param of GammaDir prior */
// defaultModel.brlensDir[1] = 20.0; /* 2nd param of invGamDir prior */
defaultModel.brlensDir[2] = 1.0; /* 3rd param of Dirichlet priors */
defaultModel.brlensDir[3] = 1.0; /* 4th param of Dirichlet priors */
strcpy(defaultModel.unconstrainedPr, "GammaDir"); /* prior on branches if unconstrained */
strcpy(defaultModel.clockPr, "Uniform"); /* prior on branch lengths if clock enforced */
defaultModel.treeAgePr.prior = standardGamma; /* calibration prior on tree age */
strcpy(defaultModel.treeAgePr.name, "Gamma(1.00,1.00)");
defaultModel.treeAgePr.priorParams[0] = 1.0;
defaultModel.treeAgePr.priorParams[1] = 1.0;
defaultModel.treeAgePr.priorParams[2] = -1.0;
defaultModel.treeAgePr.LnPriorProb = &LnPriorProbGamma_Param_Mean_Sd;
defaultModel.treeAgePr.LnPriorRatio = &LnProbRatioGamma_Param_Mean_Sd;
defaultModel.treeAgePr.min = 0.0;
defaultModel.treeAgePr.max = POS_INFINITY;
strcpy(defaultModel.clockRatePr, "Fixed"); /* prior on base subst. rate for clock trees */
defaultModel.clockRateNormal[0] = 1.0;
defaultModel.clockRateNormal[1] = 1.0;
defaultModel.clockRateLognormal[0] = 0.0; /* mean 0.0 on log scale corresponds to mean rate 1.0 */
defaultModel.clockRateLognormal[1] = 0.7; /* double or half the rate in one standard deviation */
defaultModel.clockRateGamma[0] = 1.0;
defaultModel.clockRateGamma[1] = 1.0;
defaultModel.clockRateExp = 1.0;
defaultModel.clockRateFix = 1.0;
strcpy(defaultModel.speciationPr, "Exponential"); /* prior on speciation rate (net diversification) */
defaultModel.speciationFix = 0.1;
defaultModel.speciationUni[0] = 0.0;
defaultModel.speciationUni[1] = 1000.0;
defaultModel.speciationExp = 10.0;
strcpy(defaultModel.extinctionPr, "Beta"); /* prior on extinction rate (turnover) */
defaultModel.extinctionFix = 0.5;
defaultModel.extinctionBeta[0] = 1;
defaultModel.extinctionBeta[1] = 1;
defaultModel.extinctionExp = 10.0;
strcpy(defaultModel.fossilizationPr, "Beta"); /* prior on fossilization rate (sampling proportion) */
defaultModel.fossilizationFix = 0.1;
defaultModel.fossilizationBeta[0] = 1;
defaultModel.fossilizationBeta[1] = 1;
defaultModel.fossilizationExp = 10.0;
strcpy(defaultModel.sampleStrat, "Random"); /* taxon sampling strategy */
defaultModel.sampleProb = 1.0; /* extant taxon sampling fraction */
defaultModel.birthRateShiftNum = 0; /* number of birth rate shifts */
defaultModel.deathRateShiftNum = 0; /* number of death rate shifts */
defaultModel.fossilSamplingNum = 0; /* number of fossil sampling rate shifts / slice sampling events */
strcpy(defaultModel.popSizePr, "Gamma"); /* prior on coalescence population size */
defaultModel.popSizeFix = 100.0; /* N_e = 100 */
defaultModel.popSizeUni[0] = 0.0;
defaultModel.popSizeUni[1] = 1000.0;
defaultModel.popSizeNormal[0] = 100.0;
defaultModel.popSizeNormal[1] = 30.0;
defaultModel.popSizeLognormal[0] = 4.6; /* mean on log scale corresponds to N_e = 100.0 */
defaultModel.popSizeLognormal[1] = 0.4; /* factor 10 in one standard deviation */
defaultModel.popSizeGamma[0] = 1.0; /* exponential with mean 1/10 = 0.1 */
defaultModel.popSizeGamma[1] = 10.0;
strcpy(defaultModel.popVarPr, "Equal"); /* prior on pop. size variation across tree */
strcpy(defaultModel.growthPr, "Fixed"); /* prior on coalescence growth rate prior */
defaultModel.growthFix = 0.0;
defaultModel.growthUni[0] = 0.0;
defaultModel.growthUni[1] = 100.0;
defaultModel.growthExp = 1.0;
defaultModel.growthNorm[0] = 0.0;
defaultModel.growthNorm[1] = 1.0;
strcpy(defaultModel.nodeAgePr, "Unconstrained"); /* prior on node depths */
strcpy(defaultModel.clockVarPr, "Strict"); /* prior on clock rate variation */
strcpy(defaultModel.cppRatePr, "Exponential") ; /* prior on rate of CPP for relaxed clock */
defaultModel.cppRateExp = 0.1;
defaultModel.cppRateFix = 1.0;
strcpy(defaultModel.cppMultDevPr, "Fixed"); /* prior on standard dev. of lognormal of rate multipliers of CPP rel clock */
defaultModel.cppMultDevFix = 0.4;
strcpy(defaultModel.tk02varPr, "Exponential"); /* prior on variance parameter for TK02 rel clock */
defaultModel.tk02varExp = 1.0;
defaultModel.tk02varFix = 1.0;
defaultModel.tk02varUni[0] = 0.0;
defaultModel.tk02varUni[1] = 10.0;
strcpy(defaultModel.wnvarPr, "Exponential"); /* prior on variance parameter for WN rel clock */
defaultModel.wnvarExp = 10.0;
defaultModel.wnvarFix = 0.1;
defaultModel.wnvarUni[0] = 0.0;
defaultModel.wnvarUni[1] = 10.0;
strcpy(defaultModel.igrvarPr, "Exponential"); /* prior on variance parameter for IGR rel clock */
defaultModel.igrvarExp = 1.0;
defaultModel.igrvarFix = 1.0;
defaultModel.igrvarUni[0] = 0.0;
defaultModel.igrvarUni[1] = 10.0;
strcpy(defaultModel.ilnvarPr, "Exponential"); /* prior on variance parameter for ILN rel clock */
defaultModel.ilnvarExp = 1.0;
defaultModel.ilnvarFix = 1.0;
defaultModel.ilnvarUni[0] = 0.0;
defaultModel.ilnvarUni[1] = 10.0;
strcpy(defaultModel.mixedvarPr, "Exponential"); /* prior on var parameter for IGR & ILN mixed clock */
defaultModel.mixedvarExp = 1.0;
defaultModel.mixedvarFix = 1.0;
defaultModel.mixedvarUni[0] = 0.0;
defaultModel.mixedvarUni[1] = 10.0;
strcpy(defaultModel.ratePr, "Fixed"); /* prior on rate for a partition */
defaultModel.ratePrDir = 1.0;
strcpy(defaultModel.generatePr, "Fixed"); /* prior on rate for a gene (multispecies coalescent) */
defaultModel.generatePrDir = 1.0;
defaultModel.nStates = 4; /* number of states for partition */
/* Report format settings */
strcpy(defaultModel.tratioFormat, "Ratio"); /* default format for tratio */
strcpy(defaultModel.revmatFormat, "Dirichlet"); /* default format for revmat */
strcpy(defaultModel.ratemultFormat, "Scaled"); /* default format for ratemult */
strcpy(defaultModel.treeFormat, "Brlens"); /* default format for trees */
strcpy(defaultModel.inferAncStates, "No"); /* do not infer ancestral states */
strcpy(defaultModel.inferPosSel, "No"); /* do not infer positive selection */
strcpy(defaultModel.inferSiteOmegas, "No"); /* do not infer site omega vals */
strcpy(defaultModel.inferSiteRates, "No"); /* do not infer site rates */
/* Allocate and initialize model indicator parameter names */
modelIndicatorParams = (char **) SafeCalloc (3, sizeof (char *));
modelIndicatorParams[0] = "aamodel";
modelIndicatorParams[1] = "gtrsubmodel";
modelIndicatorParams[2] = "";
/* Aamodel */
modelElementNames = (char ***) SafeCalloc (3, sizeof (char **));
modelElementNames[0] = (char **) SafeCalloc (12, sizeof (char *));
modelElementNames[0][0] = "Poisson";
modelElementNames[0][1] = "Jones";
modelElementNames[0][2] = "Dayhoff";
modelElementNames[0][3] = "Mtrev";
modelElementNames[0][4] = "Mtmam";
modelElementNames[0][5] = "Wag";
modelElementNames[0][6] = "Rtrev";
modelElementNames[0][7] = "Cprev";
modelElementNames[0][8] = "Vt";
modelElementNames[0][9] = "Blosum";
modelElementNames[0][10] = "LG";
modelElementNames[0][11] = "";
/* Gtrsubmodel */
modelElementNames[1] = (char **) SafeCalloc (204, sizeof (char *));
for (i=0; i<203; i++)
{
modelElementNames[1][i] = (char *) SafeCalloc (7, sizeof (char));
FromIndexToGrowthFxn(i, growthFxn);
for (j=0; j<6; j++)
modelElementNames[1][i][j] = '1' + growthFxn[j];
modelElementNames[1][i][j] = '\0';
}
modelElementNames[1][203] = "";
/* Termination */
modelElementNames[2] = (char **) SafeCalloc (1, sizeof(char *));
modelElementNames[2][0] = "";
/* initialize user trees */
for (i=0; i<MAX_NUM_USERTREES; i++)
userTree[i] = NULL;
numUserTrees = 0;
/* Reset translate table */
ResetTranslateTable();
/* finally reset everything dependent on a matrix being defined */
return (ReinitializeMrBayes ());
}
void PrintHeader (void)
{
MrBayesPrint ("\n\n");
MrBayesPrint (" MrBayes %s %s\n\n", VERSION_NUMBER, HOST_CPU);
MrBayesPrint (" (Bayesian Analysis of Phylogeny)\n\n");
# if defined (MPI_ENABLED)
MrBayesPrint (" (Parallel version)\n");
MrBayesPrint (" (%d processors available)\n\n", num_procs);
# endif
MrBayesPrint (" Distributed under the GNU General Public License\n\n\n");
MrBayesPrint (" Type \"help\" or \"help <command>\" for information\n");
MrBayesPrint (" on the commands that are available.\n\n");
MrBayesPrint (" Type \"about\" for authorship and general\n");
MrBayesPrint (" information about the program.\n\n\n");
}
int ReinitializeMrBayes (void)
{
/* this function resets everything dependent on a matrix */
int i;