files.list

mfold

                           Directory of files

NB: All information on the energy files is at the end of this file.

    Suboptimal RNA/DNA folding package - M. Zuker and D. H. Turner

                             Version 3.0

Makefile - Standard UNIX makefile for RNA folding programs. 

auto_ct2ps - The script takes a .ct file, splits it into single structure
             files, and runs 'naview' and 'plt22ps' on each one to
             produce (multiple) PostScript files. Uses one of the .nav
             files copied from mfold-3.0/dat into $MFOLDLIB.

batgen - This program creates input files for RNA folding. (source is
         batgen.f) This is an obsolete program that is used directly
         with nafold. It has some bugs in it when complicated
         constraints are requested.

begin.dat - Displays program name and version.

begin2.dat - Displays author and reference information.

bpin.f - Source code for a subroutine used by 'distance'. 

bpsrch.f - Source code for a subroutine used by 'distance'.

ct_compare - This program compares one secondary structure with a 
             group of others. Similar to 'scorer'.

ct_compare.f - Source code for ct_compare.

ct2bp - Program that converts a ct file into the "Madison Format"
        See: http://bioinfo.math.rpi.edu/~zukerm/rna/formats.html#BP
        and
        http://bioinfo.math.rpi.edu/~zukerm/rna/Madison.html
        (source is ct2bp.f)

ct_gcg.f - This file contains an alternte for of the ct subroutine
           in misc.f . This alternate generates ct files that
           can be read directly by GCG software.

distance.f - This program reads a ct file containing between 2 and 15
             structures and computes the distance between the first
             and all the rest or else the distance between all pairs.

efn - An independent program to compute the energies of foldings
      using a ct file as input. This program requires energy table
      input. The output consists of the computed energy of each
      folding found in the input ct file. Text  output and/or
      energy detail output are options. (source is efn.f and efn.inc)

efn2 - Similar to efn, except that this program re-evaluates the
       free energies of foldings using more realistic rules: coaxial
       stacking of adjacent helices and Jacobson-Stockmeyer theory
       for multi-branch loops. Source in c++ directory.

errata3.list - List of errata found in version 3 folding programs  
               with dates.

filter-sort - A script that removes all helices containing fewer than
              $1 base pairs (default = 3 for segments > 100) from a 
              .plot file. No optimal helices are removed. The original 
              file is overwritten!

formid.f - Source code for formid. This subroutine reads and interprets
           sequence data.

getseq.f - Almost the same as formid.f. Used with batgen.

h-num - A script that takes a .plot file containing optimal and
        suboptimal helices and replaces the 'energy' value by
        the 'h-num' value. Records are sorted in order of increasing
        h-num, ie, from 'best-determined' to 'worst-determined'.
        Uses h-num.exe, which is created from h-num.f.

manual.ps - A somewhat updated version of :
            M. Zuker, D.H. Mathews and D.H. Turner
            Algorithms and Thermodynamics for RNA Secondary Structure 
            Prediction: A Practical Guide.
            In: RNA Biochemistry and Biotechnology, J. Barcisszewski
            and B.F.C. Clark, eds., NATO ASI Series
            Kluwer Academic Publishers, 1999.

manual-html - Directory containing an html version of manual.ps

mfold - This script runs "newtemp" to create energy tables (for
        version 2.3 rules only), and then runs nafold and other
        program to create the entire output.

misc.f - Miscellaneous subroutines for both the linear and circular
         versions of the folding program.

multid.f - This subroutine reads and interprets sequence data. It
           differs from formid in that it automatically returns
           one sequence after another to the calling routine instead
           of requesting a sequence number of identifier. 

naview - Program to read in a .ct file from a folding program and
         to create a device independent plot file (.plt2) for plotting
         the structure in the file. (source naview.c)
         Included with the permission of R.E. (Bob) Bruccoleri:
         An improved algorithm for nucleic acid secondary structure display. 
         R.E. Bruccoleri and G. Heinrich 
         Comput Appl Biosci 4: 167-73 (1988) 
         This program has been altered by M. Zuker and D. Stewart

newtemp - This program reads the 37