1 /* These constants can be changed if necessary */ 2 #define NMLNGTH 10 /* required # of characters in sequence name */ 3 #define iters 50 /* how hard to try to estimate theta */ 4 #define menu true /* are we using the menu? */ 5 #define epsilon 0.0000001 /* a small number */ 6 #define thetaout false /* create "thetafile" with running tally 7 of theta estimates? */ 8 #define onebestree true /* "true" = only single bestree in file "bestree" 9 "false" = running tally of bestrees in file 10 "bestree" */ 11 #define MINTHETA 0.00001 /* low end of table */ 12 #define MAXTHETA 10.0 /* high end of table */ 13 #define THETALID 1000.0 /* maximum allowable theta */ 14 #define GLID 100000.0 /* maximum allowable g */ 15 #define EXPMIN -40.0 /* minimum value of "x" in "exp(x)" */ 16 #define EXPMAX 200.0 /* maximum value of "x" in "exp(x)" */ 17 #define EPSILON 10e-50 /* a really small number */ 18 #define REPEAT_TOLERANCE 50 /* how many times (sequentially) should the 19 exact same prior-likelihood value be 20 encountered in point estimation before 21 giving up. 22 ALSO 23 how many times do we reset huge growth */ 24 25 /* these constants are used only in dealing with the changing population 26 size */ 27 #define LHOP_TOLERANCE 10e-5 /* when to start using an approximation in 28 calculating likelihoods; the +tolerance 29 is the upper bound and -tolerance the lower */ 30 31 /* The following program constants should not be changed */ 32 #define point "." 33 #define rootlength 10000 /* length of root branch must be much 34 larger than the total height of the 35 tree */ 36 #define LINESIZE 128 /* this is actually (maximum linesize)+1 37 because of trailing '\0' */ 38 #define NUMBOOL 10 /* number of boolean tokens in parameter 39 file */ 40 #define NUMNUMBER 8 /* number of numeric (double) tokens in 41 parameter file */ 42 #define POSMAX DBL_MAX /* largest positive number */ 43 #define NEGMAX -(DBL_MAX - 1.0) /* smallest negative number */ 44 #define NUM_TYPE_CHAINS 2 /* number of different kinds of chains */ 45 #define NUMPARAMETERS 2 /* number of parameters of interest */ 46 #define baseA 0 47 #define baseC 1 48 #define baseG 2 49 #define baseT 3 50