The main program in the mfold package is named mfold . It is really a (Unix shell) script that calls a number of Fortran and C programs and puts together a reasonable output. Calling the mfold script without any command line parameters will cause the following output:
Usage is 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 ]The meaning and use of these parameters are discussed below.
 | Michael Zuker Institute for Biomedical Computing Washington University in St. Louis 1998-12-05 |