| 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 GEO_H |
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| 16 | #define GEO_H |
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| 17 | |
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| 18 | #include "utilities.h" |
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| 19 | |
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| 20 | int GEO_Main(int argc, char **argv); |
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| 21 | t_geo *GEO_Make_Geo_Basic(); |
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| 22 | void GEO_Make_Geo_Complete(int ldscape_sz,int n_dim,int n_tax,t_geo *t); |
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| 23 | void Free_Geo(t_geo *t); |
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| 24 | void GEO_Update_Fmat(t_geo *t); |
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| 25 | void GEO_Update_Sorted_Nd(t_geo *t,t_tree *tree); |
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| 26 | void GEO_Update_Occup(t_geo *t,t_tree *tree); |
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| 27 | void GEO_Update_Rmat(t_node *n,t_geo *t,t_tree *tree); |
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| 28 | phydbl GEO_Lk(t_geo *t,t_tree *tree); |
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| 29 | void GEO_Init_Tloc_Tips(t_geo *t,t_tree *tree); |
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| 30 | phydbl GEO_Total_Migration_Rate(t_node *n,t_geo *t); |
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| 31 | int GEO_Get_Arrival_Location(t_node *n,t_geo *t,t_tree *tree); |
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| 32 | void GEO_Simulate_Coordinates(int n, t_geo *t); |
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| 33 | t_tree *GEO_Simulate(t_geo *t, int n_otu); |
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| 34 | void GEO_Optimize_Sigma(t_geo *t, t_tree *tree); |
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| 35 | phydbl GEO_Wrap_Lk(t_edge *b, t_tree *tree, supert_tree *stree); |
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| 36 | void GEO_Optimize_Lambda(t_geo *t, t_tree *tree); |
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| 37 | void GEO_Init_Geo_Struct(t_geo *t); |
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| 38 | void GEO_Optimize_Tau(t_geo *t, t_tree *tree); |
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| 39 | void GEO_Get_Locations_Beneath(t_geo *t, t_tree *tree); |
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| 40 | void GEO_Get_Locations_Beneath_Post(t_node *a, t_node *d, t_geo *t, t_tree *tree); |
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| 41 | void GEO_Randomize_Locations_Pre(t_node *n, t_geo *t, t_tree *tree); |
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| 42 | void GEO_Randomize_Locations(t_node *n, t_geo *t, t_tree *tree); |
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| 43 | void GEO_Get_Sigma_Max(t_geo *t); |
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| 44 | void MCMC_Geo_Updown_Tau_Lbda(t_tree *tree); |
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| 45 | void MCMC_Geo_Updown_Lbda_Sigma(t_tree *tree); |
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| 46 | int GEO_Simulate_Estimate(int argc, char **argv); |
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| 47 | void GEO_Read_In_Landscape(char *file_name, t_geo *t, phydbl **ldscape, int **loc_hash, t_tree *tree); |
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| 48 | int GEO_Estimate(int argc, char **argv); |
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| 49 | phydbl *GEO_MCMC(t_tree *tree); |
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| 50 | |
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| 51 | #endif |
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