Searched defs:mixt_tree (Results 1 – 14 of 14) sorted by relevance
/dports/biology/phyml/phyml-3.3.20200621/src/ |
H A D | mixt.c | 20 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() [all …]
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H A D | free.c | 27 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()
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H A D | optimiz.c | 810 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() [all …]
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H A D | io.c | 3968 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()
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H A D | make.c | 1389 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()
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H A D | date.c | 38 t_tree *mixt_tree,*tree; in DATE_XML() local
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H A D | times.c | 1505 …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()
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H A D | mcmc.c | 333 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()
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H A D | rates.c | 3411 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()
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H A D | xml.c | 13 t_tree *tree,*mixt_tree,*root_tree; in XML_Process_Base() local
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H A D | spr.c | 1816 void Spr_Shuffle(t_tree *mixt_tree) in Spr_Shuffle()
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H A D | utilities.c | 6189 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()
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H A D | phyrex.c | 42 t_tree *mixt_tree,*tree; in PHYREX_XML() local
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H A D | utilities.h | 721 …struct __Tree *mixt_tree; /*! set to NULL by default. Used for mixture models */ member
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