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 ALRT_H 16 #define ALRT_H 17 18 #include "utilities.h" 19 #include "lk.h" 20 #include "optimiz.h" 21 #include "models.h" 22 #include "free.h" 23 #include "simu.h" 24 25 26 void aLRT(t_tree *tree); 27 int Check_NNI_Five_Branches(t_tree *tree); 28 int Compute_Likelihood_Ratio_Test(t_edge *tested_edge, t_tree *tree); 29 int NNI_Neigh_BL(t_edge *b_fcus, t_tree *tree); 30 void Make_Target_Swap(t_tree *tree, t_edge *b_fcus, int swaptodo); 31 phydbl Statistics_To_Probabilities(phydbl in); 32 phydbl Statistics_To_RELL(t_tree *tree); 33 phydbl Statistics_To_SH(t_tree *tree); 34 phydbl Update_Lk_At_Given_Edge_Excluding(t_edge *b_fcus, t_tree *tree, t_node *exclude); 35 36 #endif 37