| 1 | /* |
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| 2 | |
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| 3 | PHYML : a program that computes maximum likelihood phylogenies from |
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| 4 | DNA or AA homologous sequences |
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| 5 | |
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| 6 | Copyright (C) Stephane Guindon. Oct 2003 onward |
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| 7 | |
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| 8 | All parts of the source except where indicated are distributed under |
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| 9 | the GNU public licence. See http://www.opensource.org for details. |
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| 10 | |
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| 11 | */ |
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| 12 | |
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| 13 | #include <config.h> |
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| 14 | |
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| 15 | #ifndef MAKE_H |
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| 16 | #define MAKE_H |
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| 17 | |
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| 18 | #include "utilities.h" |
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| 19 | |
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| 20 | void Make_All_Edges_Lk(t_node *a,t_node *d,t_tree *tree); |
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| 21 | void Make_New_Edge_Label(t_edge *b); |
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| 22 | t_edge *Make_Edge_Light(t_node *a,t_node *d,int num); |
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| 23 | void Make_Edge_Pars(t_edge *b,t_tree *tree); |
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| 24 | void Make_Edge_Pars_Left(t_edge *b,t_tree *tree); |
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| 25 | void Make_Edge_Pars_Rght(t_edge *b,t_tree *tree); |
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| 26 | void Make_Edge_Lk(t_edge *b,t_tree *tree); |
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| 27 | void Make_Edge_Lk_Left(t_edge *b,t_tree *tree); |
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| 28 | void Make_Edge_Lk_Rght(t_edge *b,t_tree *tree); |
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| 29 | void Make_Edge_NNI(t_edge *b); |
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| 30 | nni *Make_NNI(); |
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| 31 | t_node *Make_Node_Light(int num); |
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| 32 | void Make_Node_Lk(t_node *n); |
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| 33 | nexcom **Make_Nexus_Com(); |
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| 34 | nexparm *Make_Nexus_Parm(); |
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| 35 | matrix *Make_Mat(int n_otu); |
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| 36 | t_tree *Make_Tree_From_Scratch(int n_otu,calign *data); |
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| 37 | t_tree *Make_Tree(int n_otu); |
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| 38 | void Make_Tree_Path(t_tree *tree); |
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| 39 | void Make_All_Tree_Nodes(t_tree *tree); |
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| 40 | void Make_All_Tree_Edges(t_tree *tree); |
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| 41 | calign *Make_Cseq(int n_otu,int crunch_len,int state_len,int init_len,char **sp_names); |
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| 42 | t_treelist *Make_Treelist(int list_size); |
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| 43 | t_opt *Make_Optimiz(); |
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| 44 | void Make_Custom_Model(t_mod *mod); |
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| 45 | t_mod *Make_Model_Basic(); |
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| 46 | void Make_Model_Complete(t_mod *mod); |
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| 47 | t_efrq *Make_Efrq(int ns); |
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| 48 | t_rmat *Make_Rmat(int ns); |
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| 49 | option *Make_Input(); |
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| 50 | eigen *Make_Eigen_Struct(int ns); |
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| 51 | triplet *Make_Triplet_Struct(t_mod *mod); |
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| 52 | void Make_Short_L(t_tree *tree); |
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| 53 | void Make_RAS_Complete(t_ras *ras); |
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| 54 | t_ras *Make_RAS_Basic(); |
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| 55 | void Make_Best_Spr(t_tree *tree); |
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| 56 | void Make_Spr_List(t_tree *tree); |
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| 57 | t_spr *Make_One_Spr(t_tree *tree); |
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| 58 | void Make_Tree_4_Pars(t_tree *tree, calign *cdata, int n_site); |
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| 59 | t_string *Make_String(int len); |
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| 60 | t_mcmc *MCMC_Make_MCMC_Struct(); |
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| 61 | void Make_Tree_4_Lk(t_tree *tree,calign *cdata,int n_site); |
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| 62 | t_rate *RATES_Make_Rate_Struct(int n_otu); |
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| 63 | t_cal *Make_Calib(); |
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| 64 | void Make_Efrq_Weight(t_tree *mixt_tree); |
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| 65 | void Make_Rmat_Weight(t_tree *mixt_tree); |
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| 66 | |
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| 67 | #endif |
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