source: branches/profile/GDE/PHYML/lk.h

Last change on this file was 4073, checked in by westram, 13 years ago
  • phyml 2.4.5
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 1.3 KB
Line 
1/*
2
3PHYML :  a program that  computes maximum likelihood  phylogenies from
4DNA or AA homologous sequences
5
6Copyright (C) Stephane Guindon. Oct 2003 onward
7
8All parts of  the source except where indicated  are distributed under
9the GNU public licence.  See http://www.opensource.org for details.
10
11*/
12
13#ifndef ML_H
14#define ML_H
15
16
17void Init_Tips_At_One_Site_Nucleotides(char state,double **p_lk);
18void Init_Tips_At_One_Site_AA(char aa,double **p_lk);
19void Get_All_Partial_Lk(arbre *tree,edge *b_fcus,node *a,node *d);
20void Get_All_Partial_Lk_Scale(arbre *tree,edge *b_fcus,node *a,node *d);
21void Post_Order_Lk(node *pere,node *fils,arbre *tree);
22void Pre_Order_Lk(node *pere,node *fils,arbre *tree);
23void Lk(arbre *tree,allseq *alldata);
24void Site_Lk(arbre *tree,allseq *alldata);
25double Lk_At_Given_Edge(arbre *tree,edge *b_fcus);
26void Update_P(arbre *tree,int t_edge_num);
27double Return_Lk(arbre *tree);
28double Return_Abs_Lk(arbre *tree);
29matrix *ML_Dist(allseq *data,model *mod);
30double Lk_Given_Two_Seq(allseq *data,int numseq1,int numseq2,double dist,model *mod,double *loglk,double *dloglk,double *d2loglk);
31double ***Get_Partial_Lk_Struct(arbre *tree,int len,int n_catg);
32void Unconstraint_Lk(arbre *tree);
33void Update_P_Lk(arbre *tree,edge *b_fcus,node *n);
34void Make_Tree_4_Lk(arbre *tree,allseq *alldata,int n_site);
35void Init_P_Lk_Tips(arbre *tree);
36
37
38
39#endif
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