********************************************************************/
/*
- * RCS $Id: hhfunc.h 143 2010-10-14 13:11:14Z andreas $
+ * RCS $Id: hhfunc.h 290 2013-09-20 15:18:12Z fabian $
*/
int readHMMWrapper(hmm_light *rHMM_p,
char *pcHMM_input);
void FreeHMMstruct(hmm_light *prHMM);
-int AlnToHMM2(hmm_light *rHMM_p,
+int AlnToHMM2(hmm_light *rHMM_p, hhalign_para rHhalignPara,
char **ppcSeq, int iN);
int HHMake_Wrapper(char *tmp_aln, char *hmm_out);