| 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 | #include <config.h> |
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| 14 | |
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| 15 | #ifndef NJ_H |
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| 16 | #define NJ_H |
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| 17 | |
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| 18 | #include "utilities.h" |
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| 19 | #include "optimiz.h" |
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| 20 | #include "free.h" |
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| 21 | |
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| 22 | void Bionj(matrix *mat); |
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| 23 | void Finish(matrix *mat); |
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| 24 | void Compute_Sx(matrix *mat); |
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| 25 | phydbl Sum_S(matrix *mat, int i); |
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| 26 | phydbl Dist(matrix *mat, int x, int y); |
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| 27 | phydbl Q_Agglo(matrix *mat, int x, int y); |
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| 28 | phydbl Variance(matrix *mat, int x, int y); |
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| 29 | phydbl Br_Length(matrix *mat, int x, int y); |
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| 30 | void Update_Dist(matrix *mat, int x, int y); |
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| 31 | phydbl Lamda(matrix *mat, int x, int y, phydbl vxy); |
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| 32 | void Best_Pair(matrix *mat, int *x, int *y, phydbl *score); |
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| 33 | phydbl Var_Red(matrix *mat, int x, int y, int i, phydbl lamda, phydbl vxy); |
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| 34 | void Update_Tree(matrix *mat, int x, int y, phydbl lx, phydbl ly, phydbl score); |
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| 35 | void Update_Mat(matrix *mat, int x, int y, |
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| 36 | phydbl lx, phydbl ly, phydbl vxy, phydbl lamda); |
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| 37 | phydbl Dist_Red(matrix *mat, int x, phydbl lx, int y, |
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| 38 | phydbl ly, int i, phydbl lamda); |
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| 39 | int Bionj_Br_Length_Post(t_node *a, t_node *d, matrix *mat); |
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| 40 | void Bionj_Br_Length(matrix *mat); |
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| 41 | |
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| 42 | #endif |
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