| 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_P_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_P_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 | |
|---|
| 39 | #endif |
|---|
