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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN"><!--Converted with LaTeX2HTML 98.1p1 release (March 2nd, 1998)originally by Nikos Drakos (nikos@cbl.leeds.ac.uk), CBLU, University of Leeds* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan* with significant contributions from:  Jens Lippmann, Marek Rouchal, Martin Wilck and others --><HTML><HEAD><TITLE>Running the programs</TITLE><META NAME="description" CONTENT="Running the programs"><META NAME="keywords" CONTENT="FEBS98-html"><META NAME="resource-type" CONTENT="document"><META NAME="distribution" CONTENT="global"><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1"><LINK REL="STYLESHEET" HREF="FEBS98-html.css"><LINK REL="next" HREF="node13.html"><LINK REL="previous" HREF="node6.html"><LINK REL="up" HREF="FEBS98-html.html"><LINK REL="next" HREF="node8.html"></HEAD><BODY BGCOLOR=#FFDEAD TEXT=#202020 LINK=#800000 ALINK=#ffff00 VLINK=#353976><!--Navigation Panel--><A NAME="tex2html135" HREF="node8.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html132" HREF="FEBS98-html.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html126" HREF="node6.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html134" HREF="node1.html"><IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents" SRC="img/contents_motif.gif"></A>  <BR><B> Next:</B> <A NAME="tex2html136" HREF="node8.html">COMMAND LINE PARAMETERS</A><B> Up:</B> <A NAME="tex2html133" HREF="FEBS98-html.html">Algorithms and Thermodynamics for</A><B> Previous:</B> <A NAME="tex2html127" HREF="node6.html">Constrained folding</A><BR><BR><!--End of Navigation Panel--><H1><A NAME="SECTION00070000000000000000">Running the programs</A></H1><P>The main program in the <I>mfold</I> package is named <I>mfold</I> . Itis really a (Unix shell) script that calls a number of Fortran and Cprograms and puts together a reasonable output. Calling the <I>mfold</I> script without any command line parameters will cause thefollowing output:<PRE>Usage ismfold 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
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