This new version of the software is based changes made in response to reviewer feedback. We've added a new /scripts folder that contains some Python tools that we used for this project. ligate_staple_breaks.py merges broken staples back into unbroken staple precursors to aid in optimizing old designs make_scaffold_permutations.py was used to generate permuted scaffold sequences used in Fig. S12 analysis. staple_csv_to_color_xlsx.py converts a Cadnano-exported staple csv file into an Excel xlsx file with color highlighting Full Changelog: https://github.com/douglaslab/pyOrigamiBreak/compare/v1.0.0...v1.0.1