1 /* 2 3 PhyML: a program that computes maximum likelihood phylogenies from 4 DNA or AA homologous sequences. 5 6 Copyright (C) Stephane Guindon. Oct 2003 onward. 7 8 All parts of the source except where indicated are distributed under 9 the GNU public licence. See http://www.opensource.org for details. 10 11 */ 12 13 #include <config.h> 14 15 #ifndef TIPORDER_H 16 #define TIPORDER_H 17 18 #include "times.h" 19 #include "spr.h" 20 #include "utilities.h" 21 #include "lk.h" 22 #include "optimiz.h" 23 #include "bionj.h" 24 #include "models.h" 25 #include "free.h" 26 #include "help.h" 27 #include "simu.h" 28 #include "eigen.h" 29 #include "pars.h" 30 #include "alrt.h" 31 #include "m4.h" 32 #include "draw.h" 33 #include "rates.h" 34 #include "mcmc.h" 35 #include "io.h" 36 #include "stats.h" 37 38 void TIPO_Get_Tips_Y_Rank(t_tree *tree); 39 void TIPO_Get_Tips_Y_Rank_Pre(t_node *a, t_node *d, phydbl *curr_rank, t_tree *tree); 40 void TIPO_Get_All_Y_Rank(t_tree *tree); 41 void TIPO_Get_All_Y_Rank_Pre(t_node *a, t_node *d, t_tree *tree); 42 void TIPO_Swap_One_Node(t_node *d, t_tree *tree); 43 void TIPO_Minimize_Tip_Order_Score(int n_trees, t_tree **list_tree, t_tree *ref_tree); 44 void TIPO_Print_Tip_Ordered(t_tree *ref_tree); 45 void TIPO_Print_Tip_Ordered_Pre(t_node *a, t_node *d, t_tree *ref_tree); 46 phydbl TIPO_Untangle_Tree(t_tree *tree); 47 void TIPO_Untangle_Node(t_node *a, t_node *d, t_node **node_table, int *conflict, t_tree *tree); 48 int TIPO_Untangle_Tree_List(int n_trees, t_tree **list_tree, t_tree *ref_tree); 49 int TIPO_Check_Tip_Ranks(t_tree *tree); 50 void TIPO_Read_Taxa_Coordinates(FILE *fp_coord, t_tree *tree); 51 void TIPO_Get_Tips_Y_Rank_From_Zscores(t_tree *tree); 52 void TIPO_Init_Tip_Num(t_tree *tree); 53 void TIPO_Read_Taxa_Zscores(FILE *fp_coord, t_tree *tree); 54 void TIPO_Sort_Translation_Table(t_tree *tree); 55 void TIPO_Randomize_Tip_Y_Ranks(t_tree *tree); 56 phydbl TIPO_Read_One_Taxon_Zscore(FILE *fp, char *seqname_qry, int col, t_tree *tree); 57 void TIPO_Normalize_Zscores(t_tree *tree); 58 void TIPO_Get_Min_Number_Of_Tip_Permut(t_tree *tree); 59 phydbl TIPO_Lk(t_tree *tree); 60 phydbl TIPO_Lk_Post(t_node *a, t_node *d, t_tree *tree); 61 phydbl TIPO_Lk_Core(t_node *a, t_node *d, t_tree *tree); 62 63 64 #endif 65