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