source: branches/profile/GDE/PHYML/bionj.h

Last change on this file was 4073, checked in by westram, 13 years ago
  • phyml 2.4.5
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 1.3 KB
Line 
1/*
2
3PHYML :  a program that  computes maximum likelihood  phylogenies from
4DNA or AA homologous sequences
5
6Copyright (C) Stephane Guindon. Oct 2003 onward
7
8All parts of  the source except where indicated  are distributed under
9the GNU public licence.  See http://www.opensource.org for details.
10
11*/
12
13#ifndef NJ_H
14#define NJ_H
15
16#include "utilities.h"
17#include "optimiz.h"
18/*#include "tools.h"*/
19
20void   Bionj(matrix *mat);
21void   Finish(matrix *mat);
22void   Bionj_Scores(matrix *mat);
23void   Compute_Sx(matrix *mat);
24double Sum_S(matrix *mat, int i);
25double Dist(matrix *mat, int x, int y);
26double Q_Agglo(matrix *mat, int x, int y);
27double Variance(matrix *mat, int x, int y);
28double Br_Length(matrix *mat, int x, int y);
29void   Update_Dist(matrix *mat, int x, int y);
30double Lamda(matrix *mat, int x, int y, double vxy);
31void   Best_Pair(matrix *mat, int *x, int *y, double *score);
32double Var_Red(matrix *mat, int x, int y, int i, double lamda, double vxy);
33void   Update_Tree(matrix *mat, int x, int y, double lx, double ly, double score);
34void   Update_Mat(matrix *mat, int x, int y, 
35                  double lx, double ly, double vxy, double lamda);
36double Dist_Red(matrix *mat, int x, double lx, int y, 
37                double ly, int i, double lamda);
38int    Bionj_Br_Length_Post(node *a, node *d, matrix *mat);
39void   Bionj_Br_Length(matrix *mat);
40
41#endif
Note: See TracBrowser for help on using the repository browser.