| 1 | /* |
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| 2 | |
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| 3 | PHYML : a program that computes maximum likelihood phylogenies from |
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| 4 | DNA or AA homologous sequences |
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| 5 | |
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| 6 | Copyright (C) Stephane Guindon. Oct 2003 onward |
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| 7 | |
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| 8 | All parts of the source except where indicated are distributed under |
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| 9 | the GNU public licence. See http://www.opensource.org for details. |
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| 10 | |
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| 11 | */ |
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| 12 | |
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| 13 | #ifndef OPTIMIZ_H |
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| 14 | #define OPTIMIZ_H |
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| 15 | |
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| 16 | void Optimiz_Ext_Br(arbre *tree); |
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| 17 | void Optimize_Alpha(arbre *tree); |
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| 18 | void Optimize_Kappa(arbre *tree); |
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| 19 | void Optimize_Lambda(arbre *tree); |
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| 20 | void Optimize_Param_Parall(arbre *tree); |
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| 21 | double Br_Len_NR(arbre *tree,allseq *alldata,edge *b_fcus, int n_passes); |
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| 22 | double Optimize_Branch_Quad(arbre *tree, allseq *alldata, edge *b_fcus); |
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| 23 | void Optimize_After_Hide(arbre *tree, allseq *alldata, node *h); |
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| 24 | void Round_Optimize(arbre *tree, allseq *data); |
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| 25 | void Print_Lk_Progress(arbre *tree, double lk_new, double lk_old, int n_iter); |
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| 26 | int Dist_Seq_Brak(double *ax, double *bx, double *cx, |
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| 27 | double *fa, double *fb, double *fc, |
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| 28 | allseq *data, int num1, int num2, model *mod); |
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| 29 | double Dist_Seq_Brent(double ax, double bx, double cx, double tol, |
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| 30 | double *xmin, allseq *data, |
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| 31 | int num1, int num2, model *mod); |
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| 32 | double Optimize_One_Dist(allseq *data, int numseq1, int numseq2, |
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| 33 | double init_dist, model *mod); |
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| 34 | double Kappa_Golden(double ax, double bx, double cx, double tol, |
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| 35 | double *xmin, arbre *tree, allseq *alldata); |
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| 36 | double Lambda_Golden(double ax, double bx, double cx, double tol, |
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| 37 | double *xmin, arbre *tree, allseq *alldata); |
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| 38 | double Alpha_Golden_Br_Opt(double ax, double bx, double cx, double tol, |
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| 39 | double *xmin, arbre *tree, allseq *alldata, |
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| 40 | int n_opt, double *init_l); |
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| 41 | double Alpha_Golden(double ax, double bx, double cx, double tol,double *xmin, |
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| 42 | arbre *tree, allseq *alldata); |
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| 43 | double Br_Len_Golden(double ax, double bx, double cx, double tol, |
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| 44 | double *xmin, edge *b_fcus, arbre *tree); |
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| 45 | double Br_Len_Brent(double ax, double bx, double cx, double tol, |
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| 46 | double *xmin, edge *b_fcus, arbre *tree, int n_iter_max); |
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| 47 | int Br_Len_Brak(double *ax, double *bx, double *cx, |
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| 48 | double *fa, double *fb, double *fc, |
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| 49 | edge *b_fcus, arbre *tree); |
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| 50 | double Optimize_Path_Length(model *mod, allseq *alldata, edge *a, |
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| 51 | int lra, edge *b, int lrb, double i_len); |
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| 52 | void Optimize_Param_Serie(node *a, node *d, edge *b_fcus, arbre *tree, |
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| 53 | allseq *alldata, int n_passes); |
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| 54 | double Optimize_Dist(model *mod, double init, allseq *twoseqs); |
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| 55 | double Pinvar_Golden(double ax, double bx, double cx, double tol, |
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| 56 | double *xmin, arbre *tree, allseq *alldata, int n_iter_max); |
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| 57 | void Optimize_Pinvar(arbre *tree); |
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| 58 | int Lambda_Brak(double *ax, double *bx, double *cx, |
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| 59 | double *fa, double *fb, double *fc, |
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| 60 | arbre *tree); |
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| 61 | int Kappa_Brak(double *ax, double *bx, double *cx, |
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| 62 | double *fa, double *fb, double *fc, |
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| 63 | arbre *tree); |
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| 64 | int Alpha_Brak(double *ax, double *bx, double *cx, |
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| 65 | double *fa, double *fb, double *fc, |
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| 66 | arbre *tree); |
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| 67 | int Pinvar_Brak(double *ax, double *bx, double *cx, |
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| 68 | double *fa, double *fb, double *fc, |
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| 69 | arbre *tree); |
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| 70 | void Optimiz_All_Free_Param(arbre *tree, int verbose); |
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| 71 | void Optimiz_RRparam_GTR(arbre *tree, int num_param); |
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| 72 | double RRparam_GTR_Golden(double ax, double bx, double cx, double tol, |
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| 73 | double *xmin, arbre *tree, allseq *alldata, double *param, int n_iter_max); |
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| 74 | |
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| 75 | int Powell_GTR_Param(arbre *tree, double *p, int n, double ftol); |
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| 76 | double Linmin_GTR_Param(arbre *tree,double *p, double *xi, int n); |
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| 77 | double F1dim(arbre *tree, double x, double *p, double *xi, double n); |
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| 78 | int Mnbrak_1dim(double *ax, double *bx, double *cx, |
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| 79 | double *fa, double *fb, double *fc, |
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| 80 | arbre *tree, |
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| 81 | double *p, double *xi, double n); |
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| 82 | double Brent_1dim(double ax, double bx, double cx, |
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| 83 | double tol, double *xmin, |
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| 84 | arbre *tree, |
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| 85 | double *p, double *xi, double n); |
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| 86 | |
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| 87 | int Min_With_Derivatives(arbre *tree, double *p, int n, double ftol, double step_size, |
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| 88 | double (*func) (), void (*dfunc)(), double (*linmin)()); |
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| 89 | void BFGS(arbre *tree, double *p, int n, double gtol, double step_size, |
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| 90 | double(*func)(), void (*dfunc)(), void (*lnsrch)(),int *failed); |
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| 91 | void Lnsrch_RR_Param(arbre *tree, int n, double *xold, double fold, double *g, double *p, double *x, |
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| 92 | double *f, double stpmax, int *check); |
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| 93 | void Optimize_Single_Param_Generic(arbre *tree, double *param, |
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| 94 | double start, |
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| 95 | double lim_inf, double lim_sup, |
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| 96 | int n_max_iter); |
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| 97 | int Generic_Brak(double *param, |
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| 98 | double *ax, double *bx, double *cx, |
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| 99 | double *fa, double *fb, double *fc, |
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| 100 | double lim_inf, double lim_sup, |
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| 101 | arbre *tree); |
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| 102 | double Generic_Brent(double *param, |
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| 103 | double ax, double bx, double cx, double tol, |
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| 104 | double *xmin, arbre *tree, int n_iter_max); |
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| 105 | void Optimize_Br_Len_Serie(node *a, node *d, edge *b_fcus, |
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| 106 | arbre *tree,allseq *alldata, int n_passes); |
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| 107 | void Lnsrch_Nucleotide_Frequencies(arbre *tree, int n, double *xold, |
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| 108 | double fold, double *g, double *p, double *x, |
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| 109 | double *f, double stpmax, int *check); |
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| 110 | |
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| 111 | void Optimize_Global_Rate(arbre *tree); |
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| 112 | |
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| 113 | |
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| 114 | |
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| 115 | #endif |
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| 116 | |
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