| 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 | #ifndef NJ_H |
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| 14 | #define NJ_H |
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| 15 | |
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| 16 | #include "utilities.h" |
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| 17 | #include "optimiz.h" |
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| 18 | /*#include "tools.h"*/ |
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| 19 | |
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| 20 | void Bionj(matrix *mat); |
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| 21 | void Finish(matrix *mat); |
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| 22 | void Bionj_Scores(matrix *mat); |
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| 23 | void Compute_Sx(matrix *mat); |
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| 24 | double Sum_S(matrix *mat, int i); |
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| 25 | double Dist(matrix *mat, int x, int y); |
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| 26 | double Q_Agglo(matrix *mat, int x, int y); |
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| 27 | double Variance(matrix *mat, int x, int y); |
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| 28 | double Br_Length(matrix *mat, int x, int y); |
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| 29 | void Update_Dist(matrix *mat, int x, int y); |
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| 30 | double Lamda(matrix *mat, int x, int y, double vxy); |
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| 31 | void Best_Pair(matrix *mat, int *x, int *y, double *score); |
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| 32 | double Var_Red(matrix *mat, int x, int y, int i, double lamda, double vxy); |
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| 33 | void Update_Tree(matrix *mat, int x, int y, double lx, double ly, double score); |
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| 34 | void Update_Mat(matrix *mat, int x, int y, |
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| 35 | double lx, double ly, double vxy, double lamda); |
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| 36 | double Dist_Red(matrix *mat, int x, double lx, int y, |
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| 37 | double ly, int i, double lamda); |
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| 38 | int Bionj_Br_Length_Post(node *a, node *d, matrix *mat); |
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| 39 | void Bionj_Br_Length(matrix *mat); |
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| 40 | |
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| 41 | #endif |
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