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  1. Jalview
  2. JAL-790

Ambiguity codes not supported in PID calculation for trees

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    Details

    • Type: Bug
    • Status: In Progress
    • Priority: Critical
    • Resolution: Unresolved
    • Affects Version/s: 2.8, 2.8.0b1, 2.8.1, 2.8.2, 2.9
    • Fix Version/s: None
    • Component/s: analysis
    • Labels:
      None

      Description

      The jalview %age identity tree calculation uses the Comparison.PID method, which does not take the IUBMB ambiguity codes (X, B, etc) into account when computing identity. This means that a pair of sequences containing these characters will most likely have a lower percentage identity than expected when allowing for ambiguity.

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          blocks

          Epic - Created by Jira Software - do not edit or delete. Issue type for a big user story that needs to be broken down. JAL-837 improve range of percent identity calculations and range of functions that use them

          • Major - Major loss of function.
          • Open

          Bug - A problem which impairs or prevents the functions of the product. JAL-1340 redundancy highlighting is erratic at 0% and 100%

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

          Bug - A problem which impairs or prevents the functions of the product. JAL-1312 Translation from DNA to Amino Acids fails

          • Critical - Crashes, loss of data, severe memory leak.
          • Resolved

          Improvement - An improvement or enhancement to an existing feature or task. JAL-711 Consensus line should use IUB codes

          • Major - Major loss of function.
          • Open

            Activity

              People

              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated: