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 DATE_H 16 #define DATE_H 17 18 #include "utilities.h" 19 20 int DATE_Main(int argc, char **argv); 21 void DATE_XML(char *xml_filename); 22 void DATE_Update_Secondary_Cal(t_tree *tree); 23 void DATE_Update_Secondary_Cal_Post(t_node *a, t_node *d, t_tree *tree); 24 void DATE_Update_Secondary_Cal_Pre(t_node *a, t_node *d, t_tree *tree); 25 phydbl *DATE_Splitted_Calibration(t_tree *tree); 26 void DATE_Assign_Primary_Calibration(t_tree *tree); 27 void DATE_Update_T_Prior_MinMax(t_tree *tree); 28 phydbl DATE_J(phydbl birth_r, phydbl death_r, phydbl t_min, phydbl t_pls); 29 int DATE_Is_Split_Accessible(t_node *d, int which, phydbl *splitted_cal, t_tree *tree); 30 phydbl *DATE_Splitted_Calibration(t_tree *tree); 31 phydbl DATE_J_Sum_Product(t_tree *tree); 32 int DATE_J_Sum_Product_Pre(t_node *d, int split_idx_d, int split_idx_a, phydbl prod, int fact, phydbl *total, phydbl *splitted_cal, int rk, t_tree *tree); 33 void DATE_Chain_Cal(t_tree *mixt_tree); 34 int DATE_Check_Calibration_Constraints(t_tree *tree); 35 int DATE_Check_Time_Constraints(t_tree *tree); 36 phydbl *DATE_MCMC(t_tree *tree); 37 void DATE_List_Of_Nodes_Younger_Than(t_node *a, t_node *d, phydbl lim, t_ll **list, t_tree *tree); 38 void DATE_List_Of_Nodes_And_Ancestors_Younger_Than(t_node *a, t_node *d, phydbl lim, t_ll **list, t_tree *tree); 39 t_ll *DATE_List_Of_Regraft_Nodes(t_node *prune, t_node *prune_daughter, phydbl *t_min, phydbl *t_max, int verbose, t_tree *tree); 40 phydbl DATE_Lk_Calib(t_tree *tree); 41 42 43 44 45 #endif 46