#ifndef VIENNA_RNA_PACKAGE_PROFILEALN_H
#define VIENNA_RNA_PACKAGE_PROFILEALN_H

float profile_aln(const float *T1,
                  const char  *seq1,
                  const float *T2,
                  const char  *seq2);


int set_paln_params(double  gap_open,
                    double  gap_ext,
                    double  seqweight,
                    int     free_ends);


#endif
