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 PARS_H 16 #define PARS_H 17 18 #include "utilities.h" 19 #include "lk.h" 20 #include "optimiz.h" 21 #include "models.h" 22 #include "free.h" 23 24 int Pars(t_edge *b, t_tree *tree); 25 void Post_Order_Pars(t_node *a, t_node *d, t_tree *tree); 26 void Pre_Order_Pars(t_node *a, t_node *d, t_tree *tree); 27 void Get_Partial_Pars(t_tree *tree, t_edge *b_fcus, t_node *a, t_node *d); 28 void Site_Pars(t_tree *tree); 29 void Init_Ui_Tips(t_tree *tree); 30 void Update_Partial_Pars(t_tree *tree, t_edge *b_fcus, t_node *n); 31 int Pars_At_Given_Edge(t_edge *b, t_tree *tree); 32 void Get_All_Partial_Pars(t_tree *tree, t_edge *b_fcus, t_node *a, t_node *d); 33 int Update_Pars_At_Given_Edge(t_edge *b_fcus, t_tree *tree); 34 void Init_Partial_Pars_Tips(t_tree *tree); 35 void Get_Step_Mat(t_tree *tree); 36 int Pars_Core(t_edge *b, t_tree *tree); 37 int One_Pars_Step(t_edge *b,t_tree *tree); 38 void Stepwise_Add_Pars(t_tree *tree); 39 void Backup_Partial_Pars(t_node *d, t_edge *b, t_tree *tree); 40 void Restore_Partial_Pars(t_node *d, t_edge *b, t_tree *tree); 41 42 #endif 43