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/*  (c) Centro de Regulacio Genomica                                                        */
/*  and                                                                                     */
/*  Cedric Notredame                                                                        */
/*  12 Aug 2014 - 22:07.                                                                    */
/*All rights reserved.                                                                      */
/*This file is part of T-COFFEE.                                                            */
/*                                                                                          */
/*    T-COFFEE is free software; you can redistribute it and/or modify                      */
/*    it under the terms of the GNU General Public License as published by                  */
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/*    (at your option) any later version.                                                   */
/*                                                                                          */
/*    T-COFFEE is distributed in the hope that it will be useful,                           */
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/*    GNU General Public License for more details.                                          */
/*                                                                                          */
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/*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
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/*  If you need some more information                                                       */
/*  cedric.notredame@europe.com                                                             */
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int **pavie_seq2trained_pavie_mat(Sequence *S);
double delta_matrix ( int **mat1, **mat2, char *alp);
double **pavie_seq2pavie_mat (Sequence *S, char *mat  );
int **pavie_fmat2pavie_log_mat (double **fmat, char *alphabet);
double **pavie_aln2fmat(Alignment *A, double **fmat);
Alignment* pavie_seq2pavie_msa ( Sequence *S, char *mat, char *mode);
float **pavie_seq2pavie_aln(Sequence *S,char *mat, char *mode);