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  1. Jalview
  2. JAL-4014

Add gecos generated colour schemes

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.11.2.2
    • Fix Version/s: 2.11.2.4
    • Component/s: colourschemes, gui
    • Labels:
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      Description

      https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3526-6
      (also see https://gecos.biotite-python.org/index.html )
      describes an algorithm to generate perception aware colour schemes for MSAs taking into account colour similarity (or "distance") based on known similarities between the elements (e.g. residues).

      The website publishes several colour schemes, including (see https://www.biotite-python.org/examples/gallery/sequence/color_schemes_protein.html ):
      flower -- a light colour scheme based on BLOSUM62 similarity matrix using a whole hue palette.
      blossom -- a light colour scheme with high contrast (again based on BLOSUM62)
      sunset -- a red-green colour deficiency adapted colour scheme (based on BLOSUM62)
      ocean -- a blue-shifted light colour scheme (based on BLOSUM62)

      These could be implemented in Jalview, especially the colour-constrained schemes to cater for some users with colour-perception deficiencies.

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              Assignee:
              soares Ben Soares
              Reporter:
              soares Ben Soares
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                Updated:
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