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 NJ_H 16 #define NJ_H 17 18 #include "utilities.h" 19 #include "optimiz.h" 20 #include "free.h" 21 22 void Bionj(matrix *mat); 23 void Finish(matrix *mat); 24 void Compute_Sx(matrix *mat); 25 phydbl Sum_S(matrix *mat, int i); 26 phydbl Dist(matrix *mat, int x, int y); 27 phydbl Q_Agglo(matrix *mat, int x, int y); 28 phydbl BioNJ_Variance(matrix *mat, int x, int y); 29 phydbl Br_Length(matrix *mat, int x, int y); 30 void Update_Dist(matrix *mat, int x, int y); 31 phydbl Lamda(matrix *mat, int x, int y, phydbl vxy); 32 void Best_Pair(matrix *mat, int *x, int *y, phydbl *score); 33 phydbl Var_Red(matrix *mat, int x, int y, int i, phydbl lamda, phydbl vxy); 34 void Update_Tree(matrix *mat, int x, int y, phydbl lx, phydbl ly, phydbl score); 35 void Update_Mat(matrix *mat, int x, int y, 36 phydbl lx, phydbl ly, phydbl vxy, phydbl lamda); 37 phydbl Dist_Red(matrix *mat, int x, phydbl lx, int y, 38 phydbl ly, int i, phydbl lamda); 39 int Bionj_Br_Length_Post(t_node *a, t_node *d, matrix *mat); 40 void Bionj_Br_Length(matrix *mat); 41 42 #endif 43