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Searched defs:mixt_tree (Results 1 – 14 of 14) sorted by relevance

/dports/biology/phyml/phyml-3.3.20200621/src/
H A Dmixt.c20 void MIXT_Chain_All(t_tree *mixt_tree) in MIXT_Chain_All()
65 void MIXT_Chain_Edges(t_tree *mixt_tree) in MIXT_Chain_Edges()
101 void MIXT_Chain_Nodes(t_tree *mixt_tree) in MIXT_Chain_Nodes()
135 void MIXT_Chain_Sprs(t_tree *mixt_tree) in MIXT_Chain_Sprs()
519 void MIXT_Chain_Cal(t_tree *mixt_tree) in MIXT_Chain_Cal()
2275 void MIXT_Init_Model(t_tree *mixt_tree) in MIXT_Init_Model()
2423 void MIXT_Init_T_Beg(t_tree *mixt_tree) in MIXT_Init_T_Beg()
2440 void MIXT_Init_T_End(t_tree *mixt_tree) in MIXT_Init_T_End()
2491 void MIXT_Make_Spr(t_tree *mixt_tree) in MIXT_Make_Spr()
3191 int MIXT_Part_Mixt_Size(t_tree *mixt_tree) in MIXT_Part_Mixt_Size()
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H A Dfree.c27 void Free_All_Nodes_Light(t_tree *mixt_tree) in Free_All_Nodes_Light()
46 void Free_All_Edges_Light(t_tree *mixt_tree) in Free_All_Edges_Light()
177 void Free_Tree(t_tree *mixt_tree) in Free_Tree()
337 void Free_Tree_Pars(t_tree *mixt_tree) in Free_Tree_Pars()
403 void Free_Tree_Lk(t_tree *mixt_tree) in Free_Tree_Lk()
1045 void Free_Spr_List_One_Edge(t_tree *mixt_tree) in Free_Spr_List_One_Edge()
1064 void Free_Spr_List_All_Edge(t_tree *mixt_tree) in Free_Spr_List_All_Edge()
H A Doptimiz.c810 void Optimize_Br_Len_Multiplier(t_tree *mixt_tree, int verbose) in Optimize_Br_Len_Multiplier()
2199 int Optimiz_Alpha_And_Pinv(t_tree *mixt_tree, int verbose) in Optimiz_Alpha_And_Pinv()
2748 void Optimize_RR_Params(t_tree *mixt_tree, int verbose) in Optimize_RR_Params()
2885 void Optimize_TsTv(t_tree *mixt_tree, int verbose) in Optimize_TsTv()
2949 void Optimize_Pinv(t_tree *mixt_tree, int verbose) in Optimize_Pinv()
3002 void Optimize_Alpha(t_tree *mixt_tree, int verbose) in Optimize_Alpha()
3062 void Optimize_Free_Rate(t_tree *mixt_tree, int verbose) in Optimize_Free_Rate()
3386 void Optimize_State_Freqs(t_tree *mixt_tree, int verbose) in Optimize_State_Freqs()
3495 void Optimize_Rmat_Weights(t_tree *mixt_tree, int verbose) in Optimize_Rmat_Weights()
3538 void Optimize_Efrq_Weights(t_tree *mixt_tree, int verbose) in Optimize_Efrq_Weights()
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H A Dio.c3968 void Print_Data_Structure(int final, FILE *fp, t_tree *mixt_tree) in Print_Data_Structure()
4409 t_tree *mixt_tree,*tree; in PhyML_XML() local
4560 void Check_Taxa_Sets(t_tree *mixt_tree) in Check_Taxa_Sets()
5415 json_o *JSON_Tree_To_Object(t_tree *mixt_tree) in JSON_Tree_To_Object()
5762 json_o *JSON_Tree_To_Object_Light(t_tree *mixt_tree) in JSON_Tree_To_Object_Light()
H A Dmake.c1389 void Make_Rmat_Weight(t_tree *mixt_tree) in Make_Rmat_Weight()
1471 void Make_Efrq_Weight(t_tree *mixt_tree) in Make_Efrq_Weight()
H A Ddate.c38 t_tree *mixt_tree,*tree; in DATE_XML() local
H A Dtimes.c1505 …axa(t_node **tax_list, int list_size, phydbl t_mrca, phydbl *times, int *nd_num, t_tree *mixt_tree) in TIMES_Connect_List_Of_Taxa()
1623 void TIMES_Randomize_Tree_With_Time_Constraints(t_cal *cal_list, t_tree *mixt_tree) in TIMES_Randomize_Tree_With_Time_Constraints()
H A Dmcmc.c333 void MCMC_GEO_Sigma(t_tree *mixt_tree) in MCMC_GEO_Sigma()
361 void MCMC_GEO_Lbda(t_tree *mixt_tree) in MCMC_GEO_Lbda()
388 void MCMC_GEO_Tau(t_tree *mixt_tree) in MCMC_GEO_Tau()
414 void MCMC_GEO_Dum(t_tree *mixt_tree) in MCMC_GEO_Dum()
3590 void MCMC_Kappa(t_tree *mixt_tree) in MCMC_Kappa()
3675 void MCMC_RR(t_tree *mixt_tree) in MCMC_RR()
3802 void MCMC_Free_Mixt_Rate(t_tree *mixt_tree) in MCMC_Free_Mixt_Rate()
H A Drates.c3411 void RATES_Record_Times(t_tree *mixt_tree) in RATES_Record_Times()
3436 void RATES_Reset_Times(t_tree *mixt_tree) in RATES_Reset_Times()
3672 int RATES_Check_Edge_Length_Consistency(t_tree *mixt_tree) in RATES_Check_Edge_Length_Consistency()
H A Dxml.c13 t_tree *tree,*mixt_tree,*root_tree; in XML_Process_Base() local
H A Dspr.c1816 void Spr_Shuffle(t_tree *mixt_tree) in Spr_Shuffle()
H A Dutilities.c6189 void Record_Br_Len(t_tree *mixt_tree) in Record_Br_Len()
6214 scalar_dbl **Copy_Br_Len(t_tree *mixt_tree) in Copy_Br_Len()
6248 scalar_dbl **Copy_Br_Len_Var(t_tree *mixt_tree) in Copy_Br_Len_Var()
6310 void Restore_Br_Len(t_tree *mixt_tree) in Restore_Br_Len()
H A Dphyrex.c42 t_tree *mixt_tree,*tree; in PHYREX_XML() local
H A Dutilities.h721 …struct __Tree *mixt_tree; /*! set to NULL by default. Used for mixture models */ member