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  1. Jalview
  2. JAL-1013

PCA analysis of RNA or DNA uses blosum62 matrix in calculation

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    Details

    • Type: Bug
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.8
    • Component/s: analysis, jvdesktop, jvlite, na
    • Labels:
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      Description

      PCA calculations on an RNA or DNA alignment should use either the identity matrix, or some standard nucleotide mutation matrix rather than the BLOSUM62 matrix.

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          depends on

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1027 nucleotide substitution matrix that supports rna and ambiguity codes

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Resolved
          related with

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1120 visual progress indicator when PCA calculation is running

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Resolved

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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Created:
                Updated:
                Resolved: