1 /* 2 3 PhyML: a program that computes maximum likelihood phylogenies from 4 DNA or AA homologous sequences. 5 6 Copyright (C) Stephane Guindon. Oct 2003 onward. 7 8 All parts of the source except where indicated are distributed under 9 the GNU public licence. See http://www.opensource.org for details. 10 11 */ 12 13 #include <config.h> 14 15 #ifndef SLFV_H 16 #define SLFV_H 17 18 #include "utilities.h" 19 20 phydbl SLFV_Prob_Two_Lineages_Coal(t_ldsk *l0, t_ldsk *l1, t_tree *tree); 21 phydbl SLFV_Prob_Two_Random_Lineages_Coal_One_Event(phydbl w, phydbl h, phydbl mu, phydbl rad); 22 phydbl SLFV_Coalescence_Rate(t_tree *tree); 23 phydbl SLFV_Path_Logdensity(t_ldsk *beg, t_ldsk *end, phydbl sd, t_tree *tree); 24 void SLFV_Sample_Path(t_ldsk *young, t_ldsk *old, phydbl sd, phydbl *global_hr, t_tree *tree); 25 t_ldsk *SLFV_Generate_Path(t_ldsk *beg, t_ldsk *end, phydbl n_evt, phydbl sd, t_tree *tree); 26 phydbl SLFV_Effective_Density(t_tree *tree); 27 phydbl SLFV_Rate_Per_Unit_Area(t_tree *tree); 28 phydbl SLFV_Sample_Rad_From_Prior(t_tree *tree); 29 phydbl SLFV_Update_Radius(t_tree *tree); 30 phydbl SLFV_Generation_Length(t_tree *tree); 31 phydbl SLFV_Neighborhood_Size(t_tree *tree); 32 phydbl SLFV_Update_Sigsq(t_tree *tree); 33 phydbl SLFV_Neighborhood_Size_Regression(t_tree *tree); 34 phydbl SLFV_Lk_Gaussian_Range(t_dsk *young, t_dsk *old, t_tree *tree); 35 phydbl SLFV_Lk_Gaussian(t_tree *tree); 36 phydbl SLFV_Lk_Gaussian_Core(t_dsk *disk, t_tree *tree); 37 t_sarea *SLFV_Simulate_Forward_Core(int n_sites, t_tree *tree); 38 phydbl SLFV_Simulate_Backward_Core(t_dsk *init_disk, int avoid_multiple_mergers, t_tree *tree); 39 t_tree *SLFV_Simulate(int n_otu, int n_sites, phydbl w, phydbl h, phydbl lbda, phydbl rad, phydbl mu, int r_seed); 40 t_tree *SLFV_Simulate_Independent_Loci(int n_otu, int n_loci, phydbl w, phydbl h, int r_seed); 41 void SLFV_Integrated_Coal_Rate(t_ldsk *l0, t_ldsk *l1, phydbl T, t_tree *tree); 42 void SLFV_Sum_Coal_Rate(t_ldsk *l0, t_ldsk *l1, int n, t_tree *tree); 43 phydbl SLFV_Lk_Range(t_dsk *young, t_dsk *old, t_tree *tree); 44 45 #endif 46 47 48 49 50 51