License

MIT License

Copyright (c) 2024 Allysson Allan

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Third-Party Licenses

This project uses several third-party libraries and tools, each with their own licenses:

BioPython

  • License: Biopython License (BSD-style)

  • Website: https://biopython.org/

  • Usage: Sequence processing and AB1 file handling

MAFFT

Bootstrap CSS

Chart.js

Python Standard Library

Sphinx

NumPy

Matplotlib

License Compatibility

All third-party dependencies are compatible with the MIT License used by this project. Users and contributors can freely:

  • Use the software for any purpose

  • Modify the source code

  • Distribute original or modified versions

  • Include in commercial products

  • Sublicense the software

Attributions

When using or distributing this software, please include:

  1. Copyright Notice: The original copyright notice and license

  2. Attribution: Credit to the original authors and contributors

  3. Third-Party Notices: Acknowledgment of third-party components

Example Attribution

This software uses the Sanger DNA Damage Analysis Pipeline
(https://github.com/allyssonallan/sanger_adna_damage)

Copyright (c) 2024 Allysson Allan
Licensed under the MIT License

Citation

If you use this software in academic research, please cite:

@software{sanger_adna_pipeline_2024,
  title={Sanger DNA Damage Analysis Pipeline},
  author={Farias, Allysson Allan de; LABBAT},
  year={2024},
  url={https://github.com/allyssonallan/sanger_adna_damage},
  license={MIT}
}

Or in text format:

Farias, A. A., LABBAT. (2024). Sanger DNA Damage Analysis Pipeline. GitHub. https://github.com/allyssonallan/sanger_adna_damage

Disclaimer

This software is provided “as is” without warranty of any kind. While the authors have made every effort to ensure the accuracy and reliability of the pipeline, users should:

  • Validate Results: Always validate results with independent methods

  • Understand Limitations: Be aware of the pipeline’s scope and limitations

  • Test Thoroughly: Test with known samples before using for research

  • Cite Appropriately: Give proper attribution when using in publications

The authors are not responsible for any scientific conclusions drawn from the use of this software.

Contributing

By contributing to this project, you agree that your contributions will be licensed under the same MIT License. This ensures that the project remains open and accessible to the research community.

Contact

For license-related questions or to request permission for uses not covered by the MIT License, please contact:

Updates

This license file will be updated if the project adopts additional dependencies or changes its licensing terms. Users should check the latest version in the project repository.