mfold/UNAfold

  mfold SEQ=`file_name' with optional parameters:
  [ AUX=`auxfile_name' ] [ RUN_TYPE=text (default) or html ]
  [ NA=RNA (default) or DNA ] [ LC=sequence type (default = linear) ]
  [ T=temperature (default = 37˚) ] [ P=percent (default = 5) ]
  [ W=window parameter (default - set by sequence length) ]
  [ MAXBP=max base pair distance (default - no limit) ]
  [ MAX=maximum number of foldings to be computed (default 100) ]
  [ ANN=structure annotation (default = none, p-num or ss-count) ]
  [ START=5' base # (default = 1)] [ STOP=3' base # (default = end) ]
  [ REUSE=NO/YES (default=NO) reuse existing .sav file ]