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/*  (c) Centro de Regulacio Genomica                                                        */
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/*  Cedric Notredame                                                                        */
/*  12 Aug 2014 - 22:07.                                                                    */
/*All rights reserved.                                                                      */
/*This file is part of T-COFFEE.                                                            */
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/*  cedric.notredame@europe.com                                                             */
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//sum of pairs score
double calculate_sum_of_pairs_score_affine(char *alignment_file_name, int **score_matrix, double gop, double gep);


//compare with reference alignment
void make_ref_alignment(char *seq_file_name, char *tree_file_name, char *ref_aln_name, int num_seq_in_ref);
double agreement_score(char *ref_file_name, char *aln_file_name);