/dports/biology/phyml/phyml-3.3.20200621/src/ |
H A D | beagle_utils.c | 280 double* catg_rates = float_to_double(mod->ras->gamma_rr->v, mod->ras->n_catg); in update_beagle_ras() 299 ret = beagleSetCategoryRates(mod->b_inst, mod->ras->gamma_rr->v); in update_beagle_ras()
|
H A D | lk.c | 599 len = MAX(0.0,b->l->v)*tree->mod->ras->gamma_rr->v[catg]; in Lk() 601 …if(tree->mixt_tree != NULL) len *= tree->mixt_tree->mod->ras->gamma_rr->v[tree->mod->ras->pare… in Lk() 696 rr = tree->mod->ras->gamma_rr->v[catg]; in dLk() 1815 mod->ras->gamma_rr->v[i] = 1.0; in ML_Dist() 1920 DiscreteGamma(mod->ras->gamma_r_proba->v, mod->ras->gamma_rr->v, mod->ras->alpha->v, in Lk_Given_Two_Seq() 1933 len = dist*mod->ras->gamma_rr->v[i]; in Lk_Given_Two_Seq() 2218 len = MAX(0.0,b_fcus->l->v)*tree->mod->ras->gamma_rr->v[i];//branch_len * rate in Update_PMat_At_Given_Edge() 2220 …if(tree->mixt_tree) len *= tree->mixt_tree->mod->ras->gamma_rr->v[tree->mod->ras->parent_class_nu… in Update_PMat_At_Given_Edge() 2225 …var = MAX(0.0,b_fcus->l_var->v) * POW(tree->mod->ras->gamma_rr->v[i]*tree->mod->br_len_mult->v,2); in Update_PMat_At_Given_Edge() 2226 …if(tree->mixt_tree) var *= POW(tree->mixt_tree->mod->ras->gamma_rr->v[tree->mod->ras->parent_class… in Update_PMat_At_Given_Edge() [all …]
|
H A D | make.c | 920 ras->gamma_rr = (vect_dbl *)mCalloc(1,sizeof(vect_dbl)); in Make_RAS_Basic() 921 Init_Vect_Dbl(0,ras->gamma_rr); in Make_RAS_Basic() 922 ras->gamma_rr->v = NULL; in Make_RAS_Basic() 950 ras->gamma_rr->v = (phydbl *)mCalloc(ras->n_catg,sizeof(phydbl)); in Make_RAS_Complete()
|
H A D | models.c | 685 mod->ras->gamma_rr->v, in Update_RAS() 727 … for(i=0;i<mod->ras->n_catg;i++) mod->ras->gamma_rr->v[i] = mod->ras->gamma_rr_unscaled->v[i]/sum; in Update_RAS() 731 …for(i=0;i<mod->ras->n_catg;i++) mod->ras->gamma_rr->v[i] = mod->ras->gamma_rr_unscaled->v[i] * mod… in Update_RAS()
|
H A D | io.c | 1761 sprintf(s,"P*(D|M,rr[%d]=%5.4f)",catg+1,tree->mod->ras->gamma_rr->v[catg]); in Print_Site_Lk() 1803 tree->mod->ras->gamma_rr->v[catg] * in Print_Site_Lk() 2156 for(i=0;i<mod->ras->n_catg;i++) PhyML_Printf(" %f ",mod->ras->gamma_rr->v[i]); in Print_Model() 2208 PMat(0.01*mod->ras->gamma_rr->v[k],mod,mod->ns*mod->ns*k,mod->Pij_rr->v,NULL); in Print_Model() 2209 PhyML_Printf("\n. l=%f\n",0.01*mod->ras->gamma_rr->v[k]); in Print_Model() 2390 …elative rate in class %d: \t\t%.5f [freq=%4f] \t\t",i+1,tree->mod->ras->gamma_rr->v[i],tree->mod->… in Print_Fp_Out() 2396 rk = Ranks(tree->mod->ras->gamma_rr->v,tree->mod->ras->n_catg); in Print_Fp_Out() 2401 …elative rate in class %d: \t\t%.5f [freq=%4f] \t\t",i+1,tree->mod->ras->gamma_rr->v[rk[i]],tree->m… in Print_Fp_Out() 4063 …printf(fp,"\n Relative substitution rate:\t%20f",mixt_tree->mod->ras->gamma_rr->v[tree->mod->ras… in Print_Data_Structure()
|
H A D | mixt.c | 830 len *= tree->mixt_tree->mod->ras->gamma_rr->v[tree->mod->ras->parent_class_number]; in MIXT_Lk() 2893 rr *= mixt_tree->mod->ras->gamma_rr->v[tree->mod->ras->parent_class_number]; in MIXT_dLk() 3115 …ras->n_catg;++class) PhyML_Printf("\n. rr=%f p=%f",mixt_tree->mod->ras->gamma_rr->v[class],mixt_tr… in MIXT_dLk() 3711 sprintf(s,"P*(D|M,rr[%d]=%5.4f)",catg+1,mixt_tree->mod->ras->gamma_rr->v[catg]); in MIXT_Print_Site_Lk() 3761 mixt_tree->mod->ras->gamma_rr->v[tree->mod->ras->parent_class_number] * in MIXT_Print_Site_Lk()
|
H A D | free.c | 859 Free(ras->gamma_rr->v); in Free_RAS() 867 Free(ras->gamma_rr); in Free_RAS()
|
H A D | m4.c | 631 PMat(((phydbl)(i+0.5)/step)*b->l->v*tree->mod->ras->gamma_rr->v[g],tree->mod,g*ns*ns,P1,NULL); in M4_Integral_Term_On_One_Edge() 632 …PMat(((phydbl)(step-i-0.5)/step)*b->l->v*tree->mod->ras->gamma_rr->v[g],tree->mod,g*ns*ns,P2,NULL); in M4_Integral_Term_On_One_Edge()
|
H A D | xml.c | 874 … iomod->ras->gamma_rr->v[class_number] = val; in XML_Process_Base() 2615 sprintf(val,"%f",((t_ras *)(parent->ds->obj))->gamma_rr->v[class]); in XML_Update_XML_Struct_Given_Model_Params()
|
H A D | ancestral.c | 368 rr = tree->mod->ras->gamma_rr->v[rcat]; in Map_Mutations()
|
H A D | init.c | 1063 for(i=0;i<mod->ras->n_catg;i++) mod->ras->gamma_rr->v[i] = (phydbl)i; in Init_Model() 1068 mod->ras->gamma_rr->v[0] = 1.0; in Init_Model() 1074 …for(i=0;i<mod->ras->n_catg;i++) mod->ras->gamma_rr_unscaled->v[i] = mod->ras->gamma_rr->v[i]; in Init_Model()
|
H A D | date.c | 1025 …or(i=0;i<tree->mod->ras->n_catg;i++) PhyML_Fprintf(fp_stats,"%G\t",tree->mod->ras->gamma_rr->v[i]); in DATE_MCMC()
|
H A D | utilities.h | 1049 vect_dbl *gamma_rr; /*! substitution rates defined by the RAS distribution */ member
|
H A D | phyrex.c | 903 …nt i=0;i<tree->mod->ras->n_catg;++i) PhyML_Fprintf(fp_stats,"%g\t",tree->mod->ras->gamma_rr->v[i]); in PHYREX_MCMC()
|
H A D | utilities.c | 3790 cpy->ras->gamma_rr->v[i] = ori->ras->gamma_rr->v[i]; in Record_Model()
|
H A D | mcmc.c | 2499 … for(i=0;i<tree->mod->ras->n_catg;i++) PhyML_Fprintf(fp,"%G\t",tree->mod->ras->gamma_rr->v[i]); in MCMC_Print_Param()
|