| 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 MODELS_H |
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| 16 | #define MODELS_H |
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| 17 | |
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| 18 | #include "utilities.h" |
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| 19 | #include "eigen.h" |
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| 20 | #include "free.h" |
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| 21 | #include "stats.h" |
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| 22 | #include "mixt.h" |
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| 23 | |
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| 24 | void PMat(phydbl l, t_mod *mod, int pos, phydbl *Pij); |
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| 25 | void PMat_K80(phydbl l,phydbl kappa, int pos, phydbl *Pij); |
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| 26 | void PMat_TN93(phydbl l, t_mod *mod, int pos, phydbl *Pij); |
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| 27 | void PMat_Empirical(phydbl l, t_mod *mod, int pos, phydbl *Pij); |
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| 28 | void PMat_Zero_Br_Len(t_mod *mod, int pos, phydbl *Pij); |
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| 29 | void PMat_Gamma(phydbl l, t_mod *mod, int pos, phydbl *Pij); |
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| 30 | int GetDaa (phydbl *daa, phydbl *pi, char *file_name); |
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| 31 | void Update_Qmat_GTR(phydbl *rr, phydbl *rr_val, int *rr_num, phydbl *pi, phydbl *qmat); |
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| 32 | void Update_Qmat_HKY(phydbl kappa, phydbl *pi, phydbl *qmat); |
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| 33 | void Update_Qmat_Generic(phydbl *rr, phydbl *pi, int ns, phydbl *qmat); |
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| 34 | void Translate_Custom_Mod_String(t_mod *mod); |
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| 35 | void Set_Model_Parameters(t_mod *mod); |
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| 36 | phydbl GTR_Dist(phydbl *F, phydbl alpha, eigen *eigen_struct); |
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| 37 | phydbl General_Dist(phydbl *F, t_mod *mod, eigen *eigen_struct); |
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| 38 | void Switch_From_Mod_To_M4mod(t_mod *mod); |
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| 39 | void Switch_From_M4mod_To_Mod(t_mod *mod); |
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| 40 | void PMat_JC69(phydbl l, int pos, phydbl *Pij, t_mod *mod); |
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| 41 | phydbl Get_Lambda_F84(phydbl *pi, phydbl *kappa); |
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| 42 | void Update_Eigen(t_mod *mod); |
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| 43 | void Update_RAS(t_mod *mod); |
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| 44 | void Update_Efrq(t_mod *mod); |
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| 45 | |
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| 46 | #endif |
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