| 1 | /* |
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| 2 | |
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| 3 | PHYML : a program that computes maximum likelihood phylogenies from |
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| 4 | DNA or AA homologous sequences |
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| 5 | |
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| 6 | Copyright (C) Stephane Guindon. Oct 2003 onward |
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| 7 | |
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| 8 | All parts of the source except where indicated are distributed under |
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| 9 | the GNU public licence. See http://www.opensource.org for details. |
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| 10 | |
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| 11 | */ |
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| 12 | |
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| 13 | #ifndef ML_H |
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| 14 | #define ML_H |
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| 15 | |
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| 16 | |
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| 17 | void Init_Tips_At_One_Site_Nucleotides(char state,double **p_lk); |
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| 18 | void Init_Tips_At_One_Site_AA(char aa,double **p_lk); |
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| 19 | void Get_All_Partial_Lk(arbre *tree,edge *b_fcus,node *a,node *d); |
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| 20 | void Get_All_Partial_Lk_Scale(arbre *tree,edge *b_fcus,node *a,node *d); |
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| 21 | void Post_Order_Lk(node *pere,node *fils,arbre *tree); |
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| 22 | void Pre_Order_Lk(node *pere,node *fils,arbre *tree); |
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| 23 | void Lk(arbre *tree,allseq *alldata); |
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| 24 | void Site_Lk(arbre *tree,allseq *alldata); |
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| 25 | double Lk_At_Given_Edge(arbre *tree,edge *b_fcus); |
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| 26 | void Update_P(arbre *tree,int t_edge_num); |
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| 27 | double Return_Lk(arbre *tree); |
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| 28 | double Return_Abs_Lk(arbre *tree); |
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| 29 | matrix *ML_Dist(allseq *data,model *mod); |
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| 30 | double Lk_Given_Two_Seq(allseq *data,int numseq1,int numseq2,double dist,model *mod,double *loglk,double *dloglk,double *d2loglk); |
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| 31 | double ***Get_Partial_Lk_Struct(arbre *tree,int len,int n_catg); |
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| 32 | void Unconstraint_Lk(arbre *tree); |
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| 33 | void Update_P_Lk(arbre *tree,edge *b_fcus,node *n); |
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| 34 | void Make_Tree_4_Lk(arbre *tree,allseq *alldata,int n_site); |
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| 35 | void Init_P_Lk_Tips(arbre *tree); |
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| 36 | |
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| 37 | |
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| 38 | |
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| 39 | #endif |
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| 40 | |
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| 41 | |
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| 42 | |
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