--- /dev/null
+/******************************COPYRIGHT NOTICE*******************************/
+/* (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 */
+/* the Free Software Foundation; either version 2 of the License, or */
+/* (at your option) any later version. */
+/* */
+/* T-COFFEE is distributed in the hope that it will be useful, */
+/* but WITHOUT ANY WARRANTY; without even the implied warranty of */
+/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the */
+/* GNU General Public License for more details. */
+/* */
+/* You should have received a copy of the GNU General Public License */
+/* along with Foobar; if not, write to the Free Software */
+/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */
+/*............................................... */
+/* If you need some more information */
+/* cedric.notredame@europe.com */
+/*............................................... */
+/******************************COPYRIGHT NOTICE*******************************/
+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);