.. _citations:

==================================
Citations 
==================================

`dms_tools2`_ is written by the `Bloom Lab`_.

If you use `dms_tools2`_ in your research, **please cite the following reference**:

**Bloom JD.** `"Software for the analysis and visualization of deep mutational scanning data." <http://www.biomedcentral.com/content/pdf/s12859-015-0590-4.pdf>`_. *BMC Bioinformatics*, 16:168 (2015).

    - This citation is not an up-to-date description of the current capabilities of `dms_tools2`_ (for that, see these docs) -- in fact, the citation actually describes the older `dms_tools <https://github.com/jbloom/dms_tools>`_ software. However, it is the scientific citation for `dms_tools2`_ since we are not trying to keep the citations up-to-date with the rapidly developing software. So **please cite this paper!**

Also, consider citing these papers if you use the relevant functionality:

  - The :ref:`dms2_logoplot` program utilizes a slightly modified version of the `weblogo`_ package, so if you use :ref:`dms2_logoplot` please also cite the `reference for weblogo`_.

  - If you use the `rplot module`_ to run `ggseqlogo`_, please cite the `reference for ggseqlogo`_.

  - If you use the `minimap2 module`_ to run `minimap2`_, please cite the `reference for minimap2`_.

For the full list of contributors to `dms_tools2`_, `see here <https://github.com/jbloomlab/dms_tools2/graphs/contributors>`_.
Much of the code is based on the earlier `dms_tools <https://github.com/jbloom/dms_tools>`_ software, so also `see the contributors to that earlier project <https://github.com/jbloomlab/dms_tools/graphs/contributors>`_.


.. include:: weblinks.txt