--- /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*******************************/
+/*pair wise aln implementations*/
+int myers_miller_pair_wise (Alignment *A, int *ns, int **l_s,Constraint_list *CL);
+int diff (Alignment *A, int *ns, int **ls, int s1, int M,int s2, int N , int tb, int te, Constraint_list *CL, int **pos);
+int gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+
+int sw_pair_wise (Alignment *A, int gop,int gep, int scale,int*ns, int **l_s,Constraint_list *CL, int maximise );
+Alignment ** t_coffee_lalign (Constraint_list *CL, int scale, int penalty, int maximise,Sequence *S,int sw_t, int sw_l, int sw_z, int *sw_n, int sw_io);
+
+
+Alignment * get_best_local_aln ( Alignment *A,Constraint_list *CL,int gop, int gep, int sw_t, int sw_l, int sw_z, int mode);
+Alignment * get_best_ol_local_aln ( Alignment *IN, Constraint_list*CL,int gop, int gep, int sw_t, int sw_l, int sw_z, int mode);
+Alignment * get_best_nol_local_aln ( Alignment *IN, Constraint_list*CL,int gop, int gep, int sw_t, int sw_l, int sw_z, int mode);
+
+int get_start_point ( Alignment *A,Constraint_list**CL,int gop, int gep, int T, int *first, int *last);
+
+double compute_penalty ( Constraint_list *CL, char *mode, int len);
+double compute_scale ( Constraint_list *CL, char *mode, int len);
+int evaluate_penalty (Alignment *A, Constraint_list *CL, int *scale,char *scale_mode, int *penalty, char *penalty_mode, int len_seq);
+Alignment * add_seq2aln (Constraint_list *CL,int gop,int gep, Alignment *a_list,int maximise,Sequence *S, int sw_t, int sw_l, int sw_z, int *sw_n, int sw_io);