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  1. Jalview
  2. JAL-2440

Jalview fails to load MUSCLE relaxed Clustal output

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: 2.10.1
    • Fix Version/s: None
    • Component/s: file format issue
    • Labels:
      None
    • Environment:
      macOS 10.12.3

      Description

      Using MUSCLE v3.8.31, a command line this will produce a Clustal-like alignment which Jalview 2.10.1 fails to load:

      $ muscle -in example.fasta -clw -out example.aln
      $ head -n 1 example.aln
      MUSCLE (3.8) multiple sequence alignment

      Using Muscle's strict Clustal alignment mode works:

      $ muscle -in example.fasta -clwstrict -out example.aln
      $ head -n 1 example.aln
      CLUSTAL W (1.81) multiple sequence alignment

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              Assignee:
              jprocter James Procter
              Reporter:
              peterjc Peter Cock
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                Dates

                Created:
                Updated: