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5. Methods 3 - Additional programs

Some additional programs are either distributed with the mfold package (5.1 to 5.6) or are available separately. Although the description in sections 3 and 4 was for the program lrna, the directions for using crna are identical.

• 5.1 batgen - Command file generation for batch runs
• 5.2 cttobp - Interconversion between ct files and region files
• 5.3 The distance program
• 5.4 Computing the energy of a folding
• 5.5 Creating a ``hard copy'' of an energy dot plot
• 5.6 Folding at different temperatures
• 5.7 Drawing secondary structures