| 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 | #include <config.h> |
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| 14 | |
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| 15 | #ifndef M4_H |
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| 16 | #define M4_H |
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| 17 | |
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| 18 | #include "spr.h" |
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| 19 | #include "utilities.h" |
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| 20 | #include "lk.h" |
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| 21 | #include "optimiz.h" |
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| 22 | #include "bionj.h" |
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| 23 | #include "models.h" |
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| 24 | #include "free.h" |
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| 25 | #include "help.h" |
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| 26 | #include "simu.h" |
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| 27 | #include "eigen.h" |
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| 28 | #include "pars.h" |
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| 29 | #include "alrt.h" |
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| 30 | #include "time.h" |
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| 31 | #include "draw.h" |
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| 32 | #ifdef PART |
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| 33 | #include "mg.h" |
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| 34 | #endif |
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| 35 | |
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| 36 | int M4_main(int argc, char **argv); |
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| 37 | void M4_Make_Complete(int n_h, int n_o, m4 *m4mod); |
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| 38 | m4 *M4_Make_Light(); |
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| 39 | void M4_Free_M4_Model(m4 *m4mod); |
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| 40 | void M4_Init_Qmat(m4 *m4mod, calign *data, t_mod *mod); |
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| 41 | void M4_Update_Qmat(m4 *m4mod, t_mod *mod); |
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| 42 | void M4_Init_Model(m4 *m4mod, calign *data, t_mod *mod); |
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| 43 | void M4_Init_P_Lk_Tips_Double(t_tree *tree); |
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| 44 | void M4_Init_P_Lk_Tips_Int(t_tree *tree); |
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| 45 | void M4_Post_Prob_H_Class_Edge_Site(t_edge *b, phydbl ****integral, phydbl *postprob, t_tree *tree); |
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| 46 | phydbl ****M4_Integral_Term_On_One_Edge(t_edge *b, t_tree *tree); |
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| 47 | phydbl ***M4_Compute_Proba_Hidden_States_On_Edges(t_tree *tree); |
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| 48 | void M4_Free_Integral_Term_On_One_Edge(phydbl ****integral, t_tree *tree); |
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| 49 | void M4_Compute_Posterior_Mean_Rates(phydbl ***post_probs, t_tree *tree); |
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| 50 | void M4_Scale_Br_Len(t_tree *tree); |
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| 51 | void M4_Detect_Site_Switches_Experiment(t_tree *tree); |
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| 52 | m4 *M4_Copy_M4_Model(t_mod *ori_mod, m4 *ori_m4mod); |
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| 53 | void M4_Posterior_Prediction_Experiment(t_tree *tree); |
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| 54 | void M4_Set_M4mod_Default(m4 *m4mod); |
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| 55 | phydbl **M4_Site_Branch_Classification(phydbl ***post_probs, t_tree *tree); |
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| 56 | void M4_Site_Branch_Classification_Experiment(t_tree *tree); |
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| 57 | |
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| 58 | #endif |
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