| /dports/biology/phyml/phyml-3.3.20200621/src/ |
| H A D | make.c | 584 matrix *Make_Mat(int n_otu) in Make_Mat()
615 t_tree *Make_Tree_From_Scratch(int n_otu, calign *data) in Make_Tree_From_Scratch()
650 t_tree *Make_Tree(int n_otu) in Make_Tree()
698 calign *Make_Calign(int n_otu, int crunch_len, int state_len, int init_len, char **sp_names_in, int… in Make_Calign()
1247 t_time *TIMES_Make_Time_Struct(int n_otu) in TIMES_Make_Time_Struct()
1289 t_rate *RATES_Make_Rate_Struct(int n_otu) in RATES_Make_Rate_Struct()
1616 t_phyrex_mod *PHYREX_Make_Migrep_Model(int n_otu,int dim) in PHYREX_Make_Migrep_Model()
1629 t_dsk *PHYREX_Make_Disk_Event(int n_dim, int n_otu) in PHYREX_Make_Disk_Event()
1708 void Alloc_TBE_Matrices(int n_otu, short unsigned*** i_matrix, short unsigned*** c_matrix,short uns… in Alloc_TBE_Matrices()
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| H A D | init.c | 91 void Init_Tree(t_tree *tree, int n_otu) in Init_Tree()
825 void RATES_Init_Rate_Struct(t_rate *rates, t_rate *existing_rates, int n_otu) in RATES_Init_Rate_Struct()
895 void TIMES_Init_Time_Struct(t_time *times, t_time *existing_times, int n_otu) in TIMES_Init_Time_Struct()
3489 void PHYREX_Set_Default_Migrep_Mod(int n_otu, t_phyrex_mod *t) in PHYREX_Set_Default_Migrep_Mod()
3663 void Init_Calign(int n_otu, int crunch_len, int init_len, calign *this) in Init_Calign()
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| H A D | io.c | 28 int i,n_ext,n_int,n_otu; in Read_Tree() local
160 int n_otu = tree->n_otu; in R_rtree() local
1304 void Read_Ntax_Len_Phylip(FILE *fp ,int *n_otu, int *n_tax) in Read_Ntax_Len_Phylip()
1693 void Print_Site(calign *cdata, int num, int n_otu, char *sep, int stepsize, FILE *fp) in Print_Site()
1847 void Print_Seq(FILE *fp, align **data, int n_otu) in Print_Seq()
1876 int n_otu; in Print_CSeq() local
1975 int n_otu; in Print_CSeq_Select() local
6182 int n_otu,n_dim,idx; in PHYREX_Input_Tree_Structure() local
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| H A D | invitee.c | 777 int i, j, k, f, n_otu, *indic, *n_slice, *slice_numbers; in K_Constant_Prior_Times_Log() local
1636 int n_otu; in Check_Time_Slices() local
1662 int n_otu; in Number_Of_Nodes_In_Slice() local
1687 int j, n_otu, f; in Search_Root_Node_In_Slice() local
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| H A D | slfv.c | 825 …int i,j,n_disk,n_dim,n_otu,init_pop_size,curr_pop_size,parent_id,n_lineages,sample_size,n_poly,*pe… in SLFV_Simulate_Forward_Core() local
1581 t_tree *SLFV_Simulate(int n_otu, int n_sites, phydbl w, phydbl h, phydbl lbda, phydbl rad, phydbl … in SLFV_Simulate()
1810 t_tree *SLFV_Simulate_Independent_Loci(int n_otu, int n_loci, phydbl w, phydbl h, int r_seed) in SLFV_Simulate_Independent_Loci()
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| H A D | free.c | 278 void Free_Seq(align **d, int n_otu) in Free_Seq()
1484 void Free_TBE_Matrices(int n_otu, short unsigned*** i_matrix, short unsigned*** c_matrix, in Free_TBE_Matrices()
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| H A D | geo.c | 893 t_tree *GEO_Simulate(t_geo *t, int n_otu) in GEO_Simulate()
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| H A D | rates.c | 544 void RATES_Copy_Rate_Struct(t_rate *from, t_rate *to, int n_otu) in RATES_Copy_Rate_Struct()
2856 int n_otu; in RATES_Get_Trip_Conditional_Variances() local
2894 int n_otu; in RATES_Get_All_Trip_Reg_Coeff() local
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| H A D | utilities.c | 209 int n_otu; in Compact_Data() local
407 int n_otu; in Compact_Cdata() local
1316 int i,j,n_otu; in Share_Lk_Struct() local
2040 int i,j,k,n_otu,n_rm,c_len; in Copy_Cseq() local
7036 int n_otu; in Check_Memory_Amount() local
7445 t_tree *Generate_Random_Tree_From_Scratch(int n_otu, int rooted) in Generate_Random_Tree_From_Scratch()
12387 void Shuffle_Sites(const phydbl prop, align **data, const int n_otu) in Shuffle_Sites()
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| H A D | xml.c | 923 int n_otu; in XML_Process_Base() local
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| H A D | times.c | 2260 void TIMES_Copy_Time_Struct(t_time *from, t_time *to, int n_otu) in TIMES_Copy_Time_Struct()
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| H A D | utilities.h | 757 int n_otu; /*! number of taxa */ member
996 int n_otu; /*! number of taxa */ member
1017 int n_otu; /*! number of taxa */ member
1263 int n_otu; /*! number of taxa */ member
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| H A D | phyrex.c | 4300 t_tree *PHYREX_Simulate(int n_otu, int n_sites, phydbl w, phydbl h, phydbl lbda, phydbl rad, phydb… in PHYREX_Simulate()
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| /dports/biology/seaview/seaview/csrc/ |
| H A D | phyml_util.c | 70 matrix *Make_Mat(int n_otu) in Make_Mat()
256 void Init_Tree(arbre *tree, int n_otu) in Init_Tree()
287 arbre *Make_Tree(int n_otu) in Make_Tree()
448 arbre *Make_Tree_From_Scratch(int n_otu, allseq *data) in Make_Tree_From_Scratch()
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| H A D | phyml_util.h | 262 int n_otu; /* number of taxa */ member
442 int n_otu; /* number of taxa */ member
460 int n_otu; /* number of taxa */ member
537 int n_otu; /* number of taxa */ member
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| /dports/biology/seaview/seaview/ |
| H A D | tbe.cxx | 94 void Alloc_TBE_Matrices(int n_otu, short unsigned*** i_matrix, in Alloc_TBE_Matrices()
115 void Free_TBE_Matrices(int n_otu, short unsigned*** i_matrix, short unsigned*** c_matrix, in Free_TBE_Matrices()
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| H A D | trees.cxx | 2307 char *parsimony_with_jumble(char **pars_seqs, char **pars_names, int n_otu, int njumbles, int prote… in parsimony_with_jumble()
2352 …with_bootstrap(allseq *tmpallseqs, char **pars_seqs, char **pars_names, int n_otu, int njumbles, i… in parsimony_with_bootstrap()
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| /dports/biology/iqtree/IQ-TREE-2.0.6/booster/ |
| H A D | tree.c | 1291 int n_otu = 0; in parse_nh_string() local
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