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Searched refs:phydbl (Results 1 – 25 of 73) sorted by relevance

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/dports/biology/phyml/phyml-3.3.20200621/src/
H A D	stats.h	42 phydbl Bivariate_Normal_Density(phydbl x, phydbl y, phydbl mux, phydbl muy, phydbl sdx, phydbl sdy,… 45 phydbl Pnorm(phydbl x, phydbl mean, phydbl var); 46 phydbl Dnorm_Moments(phydbl x, phydbl mean, phydbl var); 47 phydbl Dnorm(phydbl x, phydbl mean, phydbl sd); 48 phydbl Pgamma(phydbl x, phydbl shape, phydbl scale); 50 phydbl Dgamma(phydbl x, phydbl shape, phydbl scale); 65 phydbl Dnorm_Trunc(phydbl x, phydbl mean, phydbl sd, phydbl lo, phydbl up); 66 phydbl Normal_Trunc_Mean(phydbl mu, phydbl sd, phydbl min, phydbl max); 82 phydbl Norm_Trunc_Sd(phydbl mu, phydbl sd, phydbl a, phydbl b); 83 phydbl Norm_Trunc_Mean(phydbl mu, phydbl sd, phydbl a, phydbl b); [all …]
H A D	rates.h	59 phydbl RATES_Dr_X_Dx(phydbl r, phydbl mu, phydbl y, phydbl dt, phydbl a, phydbl b, phydbl lexp); 60 phydbl RATES_Dmu_Given_Y_Trpzd(phydbl mu, phydbl y, phydbl dt, phydbl a, phydbl b, phydbl lexp, 62 phydbl RATES_Dmu_Given_Y_Std(phydbl mu, phydbl y, phydbl dt, phydbl a, phydbl b, phydbl lexp); 63 phydbl RATES_Dmu_Given_Y_Romb(phydbl mu, phydbl y, phydbl dt, phydbl a, phydbl b, phydbl lexp); 64 phydbl RATES_Dmu_Given_Y(phydbl mu, phydbl y, phydbl dt, phydbl a, phydbl b, phydbl lexp); 65 phydbl RATES_Dy_Given_Mu(phydbl mu, phydbl y, phydbl dt, phydbl a, phydbl b, phydbl lexp); 66 phydbl RATES_Dmu2_Given_Y_X_Dy_Given_Mu1(phydbl mu1, phydbl mu2, phydbl y, phydbl dt1, phydbl dt2, … 67 phydbl RATES_Dmu2_Given_Mu1_Trpz(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, phydbl a, phydbl b… 69 phydbl RATES_Dmu2_And_Mu1(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, phydbl a, phydbl b, phydb… 70 phydbl RATES_Dmu2_Given_Mu1(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, phydbl a, phydbl b, phy… [all …]
H A D	optimiz.h	33 phydbl fa, phydbl fb, phydbl fc, 35 phydbl Dist_Seq_Brent(phydbl ax, phydbl bx, phydbl cx, phydbl tol, 38 phydbl Kappa_Golden(phydbl ax, phydbl bx, phydbl cx, phydbl tol, 40 phydbl Lambda_Golden(phydbl ax, phydbl bx, phydbl cx, phydbl tol, 42 phydbl Alpha_Golden_Br_Opt(phydbl ax, phydbl bx, phydbl cx, phydbl tol, 45 phydbl Alpha_Golden(phydbl ax, phydbl bx, phydbl cx, phydbl tol,phydbl xmin, 47 phydbl Br_Len_Golden(phydbl ax, phydbl bx, phydbl cx, phydbl tol, 58 phydbl Pinvar_Golden(phydbl ax, phydbl bx, phydbl cx, phydbl tol, 80 phydbl F1dim(t_tree tree, phydbl x, phydbl p, phydbl *xi, phydbl n); 85 phydbl Brent_1dim(phydbl ax, phydbl bx, phydbl cx, [all …]
H A D	lk.h	53 phydbl Lk_Dist(phydbl F, phydbl dist, t_mod mod); 81 phydbl dLk(phydbl l, t_edge b, t_tree tree); 82 phydbl Lk_Core(int state, int ambiguity_check,phydbl p_lk_left, phydbl p_lk_rght,phydbl Pij_rr,p… 84 phydbl Lk_Core_Eigen_Lr(phydbl expl, phydbl dot_prod, t_edge b, t_tree tree); 89 void Lk_dLk_Core_Eigen_Lr(phydbl expl, phydbl dot_prod, t_edge b, phydbl lk, phydbl dlk, t_tre… 90 void Lk_dLk_Core_One_Class_Eigen_Lr(phydbl dot_prod, phydbl expl, unsigned int ns, phydbl lk, ph… 91 phydbl Lk_Core_One_Class_Eigen_Lr(phydbl dot_prod, phydbl expl, int ns); 93 phydbl plk0, const phydbl plk1, const phydbl plk2, 106 phydbl Lk_Core_One_Class_No_Eigen_Lr(phydbl p_lk_left, phydbl p_lk_rght, phydbl Pij,phydbl pi, … 123 void Partial_Lk_Inin(const phydbl Pij1, const phydbl plk1, const phydbl Pij2, const phydbl *plk2… [all …]
H A D	models.h	24 void PMat(phydbl l, t_mod mod, int pos, phydbl Pij, phydbl tPij); 25 void PMat_K80(phydbl l,phydbl kappa, int pos, phydbl Pij); 26 void PMat_TN93(phydbl l, t_mod mod, int pos, phydbl Pij); 27 void PMat_Empirical(const phydbl l, const t_mod mod, const int pos, phydbl Pij, phydbl tPij); 30 int GetDaa (phydbl daa, phydbl pi, char file_name); 31 void Update_Qmat_GTR(phydbl rr, phydbl rr_val, int rr_num, phydbl pi, phydbl qmat, int opt_rr); 32 void Update_Qmat_HKY(phydbl kappa, phydbl pi, phydbl qmat); 33 void Update_Qmat_Generic(phydbl rr, phydbl pi, int ns, phydbl qmat); 36 phydbl GTR_Dist(phydbl F, phydbl alpha, eigen eigen_struct); 41 phydbl Get_Lambda_F84(phydbl pi, phydbl kappa); [all …]
H A D	utilities.h	1789 phydbl ess; 1838 phydbl val; 2011 phydbl x; 2114 void Qksort(phydbl A,phydbl B,int ilo,int ihi); 2157 void Copy_Dist(phydbl cpy,phydbl orig,int n); 2232 int Polint(phydbl xa,phydbl ya,int n,phydbl x,phydbl y,phydbl dy); 2271 phydbl Effective_Sample_Size(phydbl first_val,phydbl last_val,phydbl sum,phydbl sumsq,phydbl sumcur… 2275 phydbl Reflect(phydbl x,phydbl l,phydbl u); 2276 int Are_Equal(phydbl a,phydbl b,phydbl eps); 2298 void Joint_Proba_States_Left_Right(phydbl Pij, phydbl p_lk_left, phydbl *p_lk_rght, [all …]
H A D	avx.h	30 phydbl AVX_Lk_Core_One_Class_Eigen_Lr(const phydbl dot_prod, const phydbl expl, const unsigned in… 31 …Lk_dLk_Core_One_Class_Eigen_Lr(const phydbl dot_prod, const phydbl expl, const unsigned int ns, … 32 phydbl AVX_Lk_Core_One_Class_No_Eigen_Lr(const phydbl p_lk_left, const phydbl p_lk_rght, const ph… 33 phydbl AVX_Vect_Norm(__m256d _z); 34 phydbl AVX_Lk_Core(int state, int ambiguity_check, t_edge b, t_tree tree); 35 phydbl AVX_Lk_Core_Nucl(int state, int ambiguity_check, t_edge b, t_tree tree); 36 phydbl AVX_Lk_Core_AA(int state, int ambiguity_check, t_edge b, t_tree tree); 39 …ial_Lk_Inin(const __m256d _tPij1, const phydbl plk1, __m256d _pmat1plk1, const __m256d _tPij2,… 40 void AVX_Matrix_Vect_Prod(const __m256d _m_transpose, const phydbl _v, const int ns, __m256d re… 42 phydbl AVX_Lk_Core_One_Class_No_Eigen_Lr_Block(const phydbl p_lk_left, const phydbl *p_lk_rght, co… [all …]
H A D	eigen.h	`13 int ludcmp_1D(phydbl a, int n, phydbl d); 14 void det_1D(phydbl a, int n, phydbl d); 16 int Eigen(int job, phydbl A, int n, phydbl rr, phydbl ri, 17 phydbl vr, phydbl vi, phydbl w); 19 void unbalance(int n, phydbl vr, phydbl vi, int low, int hi, 22 phydbl vali, phydbl vr, phydbl vi); 24 phydbl vr, phydbl vi, int work); 26 int ludcmp(phydbl *a, int n, phydbl d); 27 void det(phydbl *a, int n, phydbl d); 34 complex compl (phydbl re,phydbl im); [all …]`
H A D	slfv.h	21 phydbl SLFV_Prob_Two_Random_Lineages_Coal_One_Event(phydbl w, phydbl h, phydbl mu, phydbl rad); 22 phydbl SLFV_Coalescence_Rate(t_tree tree); 23 phydbl SLFV_Path_Logdensity(t_ldsk beg, t_ldsk end, phydbl sd, t_tree tree); 24 void SLFV_Sample_Path(t_ldsk young, t_ldsk old, phydbl sd, phydbl global_hr, t_tree tree); 25 t_ldsk SLFV_Generate_Path(t_ldsk beg, t_ldsk end, phydbl n_evt, phydbl sd, t_tree tree); 26 phydbl SLFV_Effective_Density(t_tree tree); 29 phydbl SLFV_Update_Radius(t_tree tree); 32 phydbl SLFV_Update_Sigsq(t_tree tree); 35 phydbl SLFV_Lk_Gaussian(t_tree tree); 39 t_tree *SLFV_Simulate(int n_otu, int n_sites, phydbl w, phydbl h, phydbl lbda, phydbl rad, phydbl … [all …]
H A D	init.h	`39 int Init_Qmat_DCMut(phydbl daa,phydbl pi); 40 int Init_Qmat_MtArt(phydbl daa,phydbl pi); 41 int Init_Qmat_HIVb(phydbl daa,phydbl pi); 42 int Init_Qmat_HIVw(phydbl daa,phydbl pi); 43 int Init_Qmat_JTT(phydbl daa,phydbl pi); 44 int Init_Qmat_MtREV(phydbl daa,phydbl pi); 45 int Init_Qmat_LG(phydbl daa,phydbl pi); 46 int Init_Qmat_WAG(phydbl daa,phydbl pi); 47 int Init_Qmat_RtREV(phydbl daa,phydbl pi); 49 int Init_Qmat_VT(phydbl daa,phydbl pi); [all …]`
H A D	stats.c	703 phydbl Pgeom(phydbl k, phydbl p) in Pgeom() 935 phydbl Dnorm(phydbl x, phydbl mean, phydbl sd) in Dnorm() 978 phydbl Log_Dnorm_Trunc(phydbl x, phydbl mean, phydbl sd, phydbl lo, phydbl up, int *err) in Log_Dnorm_Trunc() 1025 phydbl Dnorm_Trunc(phydbl x, phydbl mean, phydbl sd, phydbl lo, phydbl up) in Dnorm_Trunc() 1131 phydbl Bivariate_Normal_Density(phydbl x, phydbl y, phydbl mux, phydbl muy, phydbl sdx, phydbl sdy,… in Bivariate_Normal_Density() 1213 phydbl Dgamma(phydbl x, phydbl shape, phydbl scale) in Dgamma() 1275 phydbl Dexp_Trunc(phydbl x, phydbl lambda, phydbl left, phydbl rght) in Dexp_Trunc() 1342 phydbl Pnorm(phydbl x, phydbl mean, phydbl sd) in Pnorm() 1542 phydbl Pgamma(phydbl x, phydbl shape, phydbl scale) in Pgamma() 3939 phydbl Norm_Trunc_Sd(phydbl mu, phydbl sd, phydbl a, phydbl b) in Norm_Trunc_Sd() [all …]
H A D	phyrex.h	23 phydbl PHYREX_Lk(t_tree tree); 24 phydbl PHYREX_Lk_RW(t_tree tree); 26 phydbl PHYREX_MCMC(t_tree tree); 52 phydbl PHYREX_Min_Radius(t_tree tree); 53 void PHYREX_Get_Min_Max_Disk_Given_Ldsk(t_dsk disk, phydbl min, phydbl max, t_tree tree); 54 void PHYREX_Get_Min_Max_Ldsk_Given_Disk(t_ldsk ldsk, phydbl min, phydbl max, t_tree tree); 63 phydbl PHYREX_LnPrior_Mu(t_tree tree); 125 phydbl PHYREX_Path_Logdensity(t_ldsk young, t_ldsk old, phydbl sd, t_tree tree); 126 void PHYREX_Sample_Path(t_ldsk young, t_ldsk old, phydbl sd, phydbl global_hr, t_tree tree); 127 t_ldsk PHYREX_Generate_Path(t_ldsk young, t_ldsk old, phydbl n_evt, phydbl sd, t_tree *tree); [all …]
H A D	bionj.h	25 phydbl Sum_S(matrix mat, int i); 26 phydbl Dist(matrix mat, int x, int y); 27 phydbl Q_Agglo(matrix mat, int x, int y); 28 phydbl BioNJ_Variance(matrix mat, int x, int y); 29 phydbl Br_Length(matrix mat, int x, int y); 31 phydbl Lamda(matrix mat, int x, int y, phydbl vxy); 33 phydbl Var_Red(matrix mat, int x, int y, int i, phydbl lamda, phydbl vxy); 34 void Update_Tree(matrix mat, int x, int y, phydbl lx, phydbl ly, phydbl score); 36 phydbl lx, phydbl ly, phydbl vxy, phydbl lamda); 37 phydbl Dist_Red(matrix *mat, int x, phydbl lx, int y, [all …]
H A D	invitee.h	9 phydbl TIMES_Calib_Cond_Prob(t_tree tree); 16 phydbl Randomize_One_Node_Time(phydbl min, phydbl max); 17 void Lk_Hastings_Ratio_Times(t_node a, t_node d, phydbl tot_prob, t_tree tree); 19 void Update_Ancestor_Cond_Jump(t_node d, phydbl L_Hast_ratio, t_tree tree); 22 phydbl K_Constant_Prior_Times_Log(t_tree tree); 24 void Check_Time_Slices(t_node a, t_node d, int result, phydbl t_cur_slice_min, phydbl t_cur_sl… 25 void Number_Of_Nodes_In_Slice(t_node d_start, t_node d, int n, phydbl t_cur_slice_min, phydbl … 26 …node d, int root_nodes, int num_elem, phydbl t_slice_min, phydbl t_slice_max, phydbl t_cur_sli… 28 phydbl Norm_Constant_Prior_Times(t_tree *tree); 36 phydbl LOG_g_i(phydbl lmbd, phydbl t_slice_max, phydbl t_slice_min, phydbl t_prior_max, phydbl t_pr… [all …]
H A D	make.c	54 tree->log_lks_aLRT = (phydbl *)mCalloc(3,sizeof(phydbl )); in Make_Tree_For_Lk() 528 n->score = (phydbl )mCalloc(3,sizeof(phydbl)); in Make_Node_Light() 593 mat->P = (phydbl )mCalloc(n_otu,sizeof(phydbl )); in Make_Mat() 975 e_frq->pi->v = (phydbl )mCalloc(ns,sizeof(phydbl)); in Make_Efrq() 1086 eig->e_val = (phydbl )mCalloc(ns,sizeof(phydbl)); in Make_Eigen_Struct() 1087 eig->e_val_im = (phydbl )mCalloc(ns,sizeof(phydbl)); in Make_Eigen_Struct() 1102 eig->r_e_vect = (phydbl )mCalloc(nsns,sizeof(phydbl)); in Make_Eigen_Struct() 1103 eig->l_e_vect = (phydbl )mCalloc(nsns,sizeof(phydbl)); in Make_Eigen_Struct() 1104 eig->dum = (phydbl )mCalloc(nsns,sizeof(phydbl)); in Make_Eigen_Struct() 1603 t->lonlat = (phydbl )mCalloc(dim,sizeof(phydbl)); in GEO_Make_Geo_Coord() [all …]
H A D	sse.h	29 phydbl SSE_Lk_Core_One_Class_Eigen_Lr(phydbl dot_prod, phydbl expl, int ns); 30 phydbl SSE_Lk_Core_One_Class_No_Eigen_Lr(phydbl p_lk_left, phydbl p_lk_rght, phydbl Pij, phydbl … 31 phydbl SSE_Lk_Core(int state, int ambiguity_check, t_edge b, t_tree tree); 32 phydbl SSE_Lk_Core_Nucl(int state, int ambiguity_check, t_edge b, t_tree tree); 33 phydbl SSE_Lk_Core_AA(int state, int ambiguity_check, t_edge b, t_tree tree); 34 void SSE_Lk_dLk_Core_One_Class_Eigen_Lr(phydbl dot_prod, phydbl expl, unsigned int ns, phydbl lk… 37 …in(const __m128d _tPij1, const int state1, const __m128d _tPij2, const phydbl _plk2, __m128d _… 38 …ial_Lk_Inin(const __m128d _tPij1, const phydbl plk1, __m128d _pmat1plk1, const __m128d _tPij2,… 39 void SSE_Matrix_Vect_Prod(const __m128d _m_transpose, const phydbl _v, const int ns, __m128d *_u);
H A D	rwrapper.h	`42 void RWRAPPER_Log_Dnorm(phydbl x, phydbl mean, phydbl sd, phydbl res); 43 …RWRAPPER_Integrated_Geometric_Brownian_Bridge_Mean(phydbl T, phydbl A, phydbl B, phydbl u, phy… 44 … RWRAPPER_Integrated_Geometric_Brownian_Bridge_Var(phydbl T, phydbl A, phydbl B, phydbl u, phy…`
H A D	date.h	25 phydbl DATE_Splitted_Calibration(t_tree tree); 28 phydbl DATE_J(phydbl birth_r, phydbl death_r, phydbl t_min, phydbl t_pls); 29 int DATE_Is_Split_Accessible(t_node d, int which, phydbl splitted_cal, t_tree tree); 30 phydbl DATE_Splitted_Calibration(t_tree tree); 31 phydbl DATE_J_Sum_Product(t_tree tree); 32 …duct_Pre(t_node d, int split_idx_d, int split_idx_a, phydbl prod, int fact, phydbl total, phydbl… 36 phydbl DATE_MCMC(t_tree tree); 37 void DATE_List_Of_Nodes_Younger_Than(t_node a, t_node d, phydbl lim, t_ll *list, t_tree tree); 38 void DATE_List_Of_Nodes_And_Ancestors_Younger_Than(t_node a, t_node d, phydbl lim, t_ll *list, t… 39 t_ll DATE_List_Of_Regraft_Nodes(t_node prune, t_node prune_daughter, phydbl t_min, phydbl t_ma… [all …]
H A D	times.h	28 void TIMES_Least_Square_Node_Times_Pre(t_node a, t_node d, phydbl A, phydbl b, int n, t_tree t… 49 phydbl TIMES_Log_Yule(t_tree tree); 50 phydbl TIMES_Lk_Times(int verbose, t_tree tree); 51 void TIMES_Lk_Times_Trav(t_node a, t_node d, phydbl lim_inf, phydbl lim_sup, phydbl logdens, t_t… 54 phydbl TIMES_Lk_Uniform_Core(t_tree tree); 65 phydbl TIMES_Lk_Yule_Root_Marginal(t_tree tree); 66 phydbl TIMES_Lk_Yule_Joint(t_tree tree); 68 phydbl TIMES_Lk_Yule_Order(t_tree tree); 77 phydbl TIMES_Lk_Birth_Death_One_Node(phydbl t, phydbl min, phydbl max, t_tree tree); 88 phydbl TIMES_Tree_Length(t_tree tree); [all …]
H A D	rwrapper.c	`66 void RWRAPPER_Log_Dnorm(phydbl x, phydbl mean, phydbl sd, phydbl res) in RWRAPPER_Log_Dnorm() 75 …RWRAPPER_Integrated_Geometric_Brownian_Bridge_Mean(phydbl T, phydbl A, phydbl B, phydbl u, phy… in RWRAPPER_Integrated_Geometric_Brownian_Bridge_Mean() 82 … RWRAPPER_Integrated_Geometric_Brownian_Bridge_Var(phydbl T, phydbl A, phydbl B, phydbl u, phy… in RWRAPPER_Integrated_Geometric_Brownian_Bridge_Var()`
H A D	mcmc.h	70 void MCMC_Single_Param_Generic(phydbl val, 71 phydbl lim_inf, 72 phydbl lim_sup, 74 phydbl lnPrior, 75 phydbl lnLike, 85 int Get_Param_Num(t_mcmc mcmc, phydbl param); 110 void MCMC_Make_Move(phydbl cur, phydbl new, phydbl inf, phydbl sup, phydbl loghr, phydbl tune, i… 142 void MCMC_PHYREX_Delete_Disk(phydbl hr, int n_delete_disks, phydbl cur_lbda, phydbl cur_mu, phydbl … 143 void MCMC_PHYREX_Insert_Disk(phydbl hr, int n_insert_disks, phydbl cur_lbda, phydbl cur_mu, phydbl … 145 void MCMC_PHYREX_Insert_Hit(phydbl hr, int n_delete_disks, phydbl cur_lbda, phydbl cur_rad, phydbl … [all …]
H A D	rates.c	99 phydbl RATES_Lk_Rates_Core(phydbl br_r_a, phydbl br_r_d, phydbl nd_r_a, phydbl nd_r_d, int n_a, int… in RATES_Lk_Rates_Core() 374 phydbl RATES_Compound_Core(phydbl mu1, phydbl mu2, int n1, int n2, phydbl dt1, phydbl dt2, phydbl a… in RATES_Compound_Core() 390 phydbl RATES_Compound_Core_Marginal(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, phydbl alpha, p… in RATES_Compound_Core_Marginal() 881 phydbl RATES_Dmu_One(phydbl mu, phydbl dt, phydbl a, phydbl b, phydbl lexp) in RATES_Dmu_One() 1175 phydbl RATES_Dmu1_And_Mu2_One_Jump_Two_Intervals(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, ph… in RATES_Dmu1_And_Mu2_One_Jump_Two_Intervals() 1204 phydbl RATES_Dmu1_Given_V_And_N(phydbl mu1, phydbl v, int n, phydbl dt1, phydbl a, phydbl b) in RATES_Dmu1_Given_V_And_N() 1278 phydbl RATES_Dmu2_And_Mu1_Given_Min_N(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, int n_min, ph… in RATES_Dmu2_And_Mu1_Given_Min_N() 1327 phydbl RATES_Dmu2_And_Mu1_Given_N(phydbl mu1, phydbl mu2, phydbl dt1, phydbl dt2, int n, phydbl a, … in RATES_Dmu2_And_Mu1_Given_N() 3087 phydbl RATES_Find_Max_Dt_Bisec(phydbl r, phydbl r_mean, phydbl ta, phydbl tc, phydbl nu, phydbl thr… in RATES_Find_Max_Dt_Bisec() 3146 phydbl RATES_Find_Min_Dt_Bisec(phydbl r, phydbl r_mean, phydbl ta, phydbl tc, phydbl nu, phydbl thr… in RATES_Find_Min_Dt_Bisec() [all …]
H A D	models.c	23 void PMat_JC69(phydbl l, int pos, phydbl Pij, t_mod mod) in PMat_JC69() 45 void PMat_K80(phydbl l, phydbl kappa, int pos, phydbl Pij) in PMat_K80() 85 void PMat_TN93(phydbl l, t_mod mod, int pos, phydbl Pij) in PMat_TN93() 169 phydbl Get_Lambda_F84(phydbl pi, phydbl kappa) in Get_Lambda_F84() 249 void PMat_Empirical(const phydbl l, const t_mod mod, const int pos, phydbl Pij, phydbl tPij) in PMat_Empirical() 410 void PMat(phydbl l, t_mod mod, int pos, phydbl Pij, phydbl tPij) in PMat() 485 void Update_Qmat_Generic(phydbl rr, phydbl pi, int ns, phydbl qmat) in Update_Qmat_Generic() 545 void Update_Qmat_GTR(phydbl rr, phydbl rr_val, int rr_num, phydbl pi, phydbl qmat, int opt_rr) in Update_Qmat_GTR() 601 void Update_Qmat_HKY(phydbl kappa, phydbl pi, phydbl qmat) in Update_Qmat_HKY() 991 void PMat_MGF_Gamma(phydbl Pij, phydbl shape, phydbl scale, phydbl scaling_fact, t_mod *mod) in PMat_MGF_Gamma() [all …]
/dports/biology/seaview/seaview/csrc/
H A D	phyml_util.h	`141 typedef double phydbl; typedef 161 phydbl dist_to_root; 218 phydbl sum_scale_f_left; 219 phydbl sum_scale_f_rght; 225 phydbl dist_btw_edges; 305 phydbl dnorm_thresh; 441 phydbl obs_pinvar; 501 phydbl alpha_old; 502 phydbl kappa_old; 503 phydbl lambda_old; [all …]`
H A D	bionj.c	55 phydbl Lamda(matrix mat, int x, int y, phydbl vxy); 57 phydbl Var_Red(matrix mat, int x, int y, int i, phydbl lamda, phydbl vxy); 58 void Update_Tree(matrix mat, int x, int y, phydbl lx, phydbl ly, phydbl score); 60 phydbl lx, phydbl ly, phydbl vxy, phydbl lamda); 61 phydbl Dist_Red(matrix mat, int x, phydbl lx, int y, 62 phydbl ly, int i, phydbl lamda); 155 void Update_Mat(matrix mat, int x, int y, phydbl lx, phydbl ly, phydbl vxy, phydbl lamda) in Update_Mat() 182 void Update_Tree(matrix mat, int x, int y, phydbl lx, phydbl ly, phydbl score) in Update_Tree() 374 phydbl Dist_Red(matrix mat, int x, phydbl lx, int y, phydbl ly, int i, phydbl lamda) in Dist_Red() 384 phydbl Var_Red(matrix mat, int x, int y, int i, phydbl lamda, phydbl vxy) in Var_Red() [all …]

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