/dports/biology/phyml/phyml-3.3.20200621/src/ |
H A D | m4.c | 285 m4 *m4mod; in M4_Make_Light() local 348 …DiscreteGamma(m4mod->h_fq,m4mod->multipl,m4mod->alpha,m4mod->alpha,m4mod->n_h,mod->ras->gamma_medi… in M4_Update_Qmat() 354 for(i=0;i<mod->m4mod->n_h;i++) mod->m4mod->h_fq[i] = FABS(mod->m4mod->h_fq_unscaled[i])/sum; in M4_Update_Qmat() 386 for(i=0;i<mod->m4mod->n_h;i++) sum += mod->m4mod->multipl[i] * mod->m4mod->h_fq[i]; in M4_Update_Qmat() 437 Update_Qmat_Generic(m4mod->o_rr, m4mod->o_fq, m4mod->n_o, m4mod->o_mats[0]); in M4_Update_Qmat() 442 …for(i=1;i<m4mod->n_h;i++) For(j,n_o*n_o) m4mod->o_mats[i][j] = m4mod->o_mats[0][j]*m4mod->multipl[… in M4_Update_Qmat() 476 Update_Qmat_Generic(m4mod->h_rr, m4mod->h_fq, m4mod->n_h, m4mod->h_mat); in M4_Update_Qmat() 481 For(i,n_h*n_h) m4mod->h_mat[i] *= m4mod->delta; in M4_Update_Qmat() 529 dim2 = tree->mod->m4mod->n_h * tree->mod->m4mod->n_o; in M4_Init_Partial_Lk_Tips_Double() 572 dim2 = tree->mod->m4mod->n_h * tree->mod->m4mod->n_o; in M4_Init_Partial_Lk_Tips_Int() [all …]
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H A D | m4.h | 37 void M4_Make_Complete(int n_h, int n_o, m4 *m4mod); 39 void M4_Free_M4_Model(m4 *m4mod); 40 void M4_Init_Qmat(m4 *m4mod, calign *data, t_mod *mod); 41 void M4_Update_Qmat(m4 *m4mod, t_mod *mod); 42 void M4_Init_Model(m4 *m4mod, calign *data, t_mod *mod); 54 void M4_Set_M4mod_Default(m4 *m4mod);
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H A D | cl.c | 573 io->mod->m4mod->use_cov_alpha = NO; in Read_Command_Line() 574 io->mod->m4mod->use_cov_free = YES; in Read_Command_Line() 588 io->mod->m4mod->n_h = (int)atoi(optarg); in Read_Command_Line() 590 if(io->mod->m4mod->n_h < 1) in Read_Command_Line() 604 io->mod->m4mod->use_cov_alpha = YES; in Read_Command_Line() 605 io->mod->m4mod->use_cov_free = NO; in Read_Command_Line() 611 io->mod->m4mod->alpha = 1.0; in Read_Command_Line() 617 if(io->mod->m4mod->alpha < 1.E-5) in Read_Command_Line() 636 io->mod->m4mod->delta = 1.0; in Read_Command_Line() 790 io->mod->m4mod->n_o = 4; in Read_Command_Line() [all …]
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H A D | init.c | 3724 mod->ns = m4mod->n_o * m4mod->n_h; in M4_Init_Model() 3730 For(i,(int)(m4mod->n_h)) m4mod->multipl[i] = 1.; in M4_Init_Model() 3733 for(i=0;i<m4mod->n_o-1;i++) in M4_Init_Model() 3737 m4mod->o_rr[ct] = MAX(mod->r_mat->qmat->v[i*m4mod->n_o+j],1.E-5); in M4_Init_Model() 3742 For(i,(int)(m4mod->n_h*(m4mod->n_h-1)/2)) m4mod->h_rr[i] = 1.; in M4_Init_Model() 3743 fq = (phydbl)(1./m4mod->n_h); in M4_Init_Model() 3747 for(i=0;i<m4mod->n_h;i++) m4mod->h_fq[i] = fq; in M4_Init_Model() 3748 for(i=0;i<m4mod->n_h;i++) m4mod->h_fq_unscaled[i] = 1.0; in M4_Init_Model() 3749 for(i=0;i<m4mod->n_h;i++) m4mod->multipl[i] = (phydbl)i; in M4_Init_Model() 3750 for(i=0;i<m4mod->n_h;i++) m4mod->multipl_unscaled[i] = (phydbl)i; in M4_Init_Model() [all …]
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H A D | models.c | 982 mod->ns = mod->m4mod->n_o; in Switch_From_M4mod_To_Mod() 983 for(i=0;i<mod->ns;i++) mod->e_frq->pi->v[i] = mod->m4mod->o_fq[i]; in Switch_From_M4mod_To_Mod() 1049 mod->ns = mod->m4mod->n_o * mod->m4mod->n_h; in Switch_From_Mod_To_M4mod() 1050 …0;i<mod->ns;i++) mod->e_frq->pi->v[i] = mod->m4mod->o_fq[i%mod->m4mod->n_o] * mod->m4mod->h_fq[i/m… in Switch_From_Mod_To_M4mod()
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H A D | interface.c | 111 io->mod->ns *= io->mod->m4mod->n_h; in Launch_Interface() 113 M4_Make_Complete(io->mod->m4mod->n_h, in Launch_Interface() 114 io->mod->m4mod->n_o, in Launch_Interface() 115 io->mod->m4mod); in Launch_Interface() 128 io->mod->m4mod->use_cov_alpha = 0; in Launch_Interface() 129 io->mod->m4mod->use_cov_free = 1; in Launch_Interface()
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H A D | init.h | 75 void M4_Init_Model(m4 *m4mod, calign *data, t_mod *mod);
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H A D | mcmc.c | 2507 for(i=0;i<tree->mod->m4mod->n_h;i++) PhyML_Fprintf(fp,"%G\t",tree->mod->m4mod->h_fq[i]); in MCMC_Print_Param() 2508 for(i=0;i<tree->mod->m4mod->n_h;i++) PhyML_Fprintf(fp,"%G\t",tree->mod->m4mod->multipl[i]); in MCMC_Print_Param() 2940 if(tree->mod->m4mod->n_h == 1) return; in MCMC_Randomize_Covarion_Rates() 2944 for(i=0;i<tree->mod->m4mod->n_h;i++) in MCMC_Randomize_Covarion_Rates() 2959 tree->mod->m4mod->delta = Uni()*(10.-0.01)+0.01; in MCMC_Randomize_Covarion_Switch() 4015 class = Rand_Int(0,tree->mod->m4mod->n_h-1); in MCMC_Covarion_Rates() 4026 max = tree->mod->m4mod->multipl_unscaled[1]; in MCMC_Covarion_Rates() 4028 else if(class == tree->mod->m4mod->n_h-1) in MCMC_Covarion_Rates() 4030 min = tree->mod->m4mod->multipl_unscaled[tree->mod->m4mod->n_h-2]; in MCMC_Covarion_Rates() 4035 …min = MIN(tree->mod->m4mod->multipl_unscaled[class-1],tree->mod->m4mod->multipl_unscaled[class+1]); in MCMC_Covarion_Rates() [all …]
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H A D | optimiz.c | 1037 Generic_Brent_Lk(&(tree->mod->m4mod->delta), in Optimiz_All_Free_Param() 1047 PhyML_Printf("[%10f]",tree->mod->m4mod->delta); in Optimiz_All_Free_Param() 1061 for(rcat=0;rcat<tree->mod->m4mod->n_h;rcat++) in Optimiz_All_Free_Param() 1069 Generic_Brent_Lk(&(tree->mod->m4mod->multipl_unscaled[rcat]), in Optimiz_All_Free_Param() 1079 PhyML_Printf("[%10f]",tree->mod->m4mod->multipl[rcat]); in Optimiz_All_Free_Param() 1083 for(rcat=0;rcat<tree->mod->m4mod->n_h;rcat++) in Optimiz_All_Free_Param() 1092 Generic_Brent_Lk(&(tree->mod->m4mod->h_fq_unscaled[rcat]), in Optimiz_All_Free_Param() 1103 PhyML_Printf("[%10f]",tree->mod->m4mod->h_fq[rcat]); in Optimiz_All_Free_Param() 1122 Generic_Brent_Lk(&(tree->mod->m4mod->alpha), in Optimiz_All_Free_Param() 1133 PhyML_Printf("[%10f]",tree->mod->m4mod->alpha); in Optimiz_All_Free_Param() [all …]
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H A D | invitee.c | 45 m4 *m4mod; in PhyTime_XML() local 71 m4mod = (m4 *)M4_Make_Light(); in PhyTime_XML() 542 if(io -> mod -> use_m4mod) M4_Init_Model(mod -> m4mod, cdata, mod); in PhyTime_XML() 677 tree -> mod -> m4mod = m4mod; in PhyTime_XML()
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H A D | main.c | 146 if(io->mod->use_m4mod) M4_Init_Model(mod->m4mod,cdata,mod); in main()
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H A D | utilities.h | 1101 struct __M4 *m4mod; member
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