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  1. Jalview
  2. JAL-303

export alignment as plain or simply formatted text

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    Details

    • Type: New Feature
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: Feature Request
    • Labels:
      None
    • Mantis ID:
      22101

      Description

      Jalview feature request submitted by:
      From: "Rudi Grams" <rgrams@gmx.net>
      To: <help@jalview.org>
      Subject: JalView -plain text export
      Date: Fri, 18 May 2007 14:34:40 +0700
      It would be very helpful if Jalview can export alignments as plain text
      with options to:

      1 show all amino acid residues of all sequences
      2 only residues different to a reference sequence
      2.1 with the suboption to distinguish between similar/non-similar residues

      Normally this is done by dots for identical and upper/lowercase
      characters for similar/non-similar.

      Such feature would make it much easier to include alignments in
      publications which do not accept coloured figures but insist on some
      kind of differentiation between identical/similar/non-similar. EMBOSS
      showalign can do this but it does not provide separate numbering for
      each sequence.

      Many thanks,

      Rudi

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            Unassigned Unassigned
            Reporter:
            jprocter Jim Procter
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              Created:
              Updated: