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Latest improvements in CLC Sequence Viewer

CLC Sequence Viewer 7.6

Release date: February 24, 2015

New features and improvements

  • A 3D Molecule Viewer is now available for visualization of protein, RNA, DNA, and small molecules.
  • Improved reporting of errors related to low disk space.

Bug fixes

  • Fixed problem with links and text in tables that were being cut off when succeeding a link.
  • Restriction site analysis: The values "Cut position(s)" column of the restriction site analysis table now behaves like numbers instead of text, meaning sorting and filtering works.
  • A problem with saved table settings that sometimes did not work has been fixed. The bug fix includes a more robust/generic way of saving table settings with different columns. To fix this problem, existing saved table settings should first be loaded on an object where it works (i.e. has the same columns as when it was saved); and then the table settings should be saved with the old name to overwrite the settings. 

  • Metadata for phylogenetic trees: A bug has been fixed with import of metadata containing column names with colons.

  • Fixed error when showing protein translations of annotations shorter than 3 bases.

CLC Sequence Viewer 7.5

Release date: August 28, 2014

New features and improvements

  • The unused "Workflows" button has been removed from the toolbar.
  • Local Search enabled from the menu bar now includes filtering on "Path".
  • Advanced filtering on tables now includes the option to filter for a space, comma or semi-colon delimited lists of terms.
  • Zoom tools redesign: The “Zoom to selection” feature is now also available for sequences, sequence lists, alignments, and read mappings.
  • Saving/applying side-panel settings for tables now works for different tables that share some columns. 
  • Copy operations can now be stopped.

  • Import of Example Data and imports done through dragging files into the workbench and dropping them in the Navigation Area will no longer block the user interface while executing. Instead, the import happens as a background process that can be monitored and controlled via the Processes tab in the lower left corner.

  • CLC workbenches now support high resolution displays such as Apple retina displays of all data shown in the View Area (including tooltips).
  • More informative naming of coding region translations produced by the tool Translate to Protein. The name for a coding region translation consists of the name of the input sequence followed by the annotation type and finally the annotation name.


  • Due to upgrade to Java 7,  Windows Server 2003 and OSX 10.5.8, 10.6 are no longer supported by Oracle. Hence, the system requirements are now: Linux, Windows Vista, Windows 7, Windows 8 or Windows Server 2008, or Mac OS X 10.7 or later.

CLC Sequence Viewer 7.0.1

Release date: March 14, 2014

New features and improvements

  • Translate to Protein (Batch Process):
    • The wizard now has options for specifying whether to translate the coding regions or extract translations from the annotations
    • The log has been made more detailed and informative
    • If the result is just a single protein sequence, the output will be just that, otherwise all sequences are output as a list
    • If the tool estimates that the number of protein sequences to be produced is greater than 1.000.000, it will create protein sequences without history, and it will not copy the common name, latin name, and taxonomy fields
  • Fasta export now reports progress while executing

Bug fixes

  • Fixed missing icon for "Metadata Import" in the phylogenetic tree table

CLC Sequence Viewer 7.0

Release date: February 11, 2014

New features and improvements

  • Complete redesign of the graphical user interface including:

    • New tool bar graphics
    • New product logos and colors, including splash screen
    • New background graphics on canvas and in dialogs
    • Tool bar has been re-organized
    • New tab design. Aligning the look and feel across platforms, which is particularly important to mac-users as split screen used to take up a lot of screen space.
  • New concept for Side Panels and Views:
    • Support for multiple screens: views can be moved to a different screen by dragging the tab of the view
    • Side Panels now consist of palettes that can be organized in group and the order can be customized
    • Palettes can be detached and placed anywhere on the screen
    • Navigation Area and Toolbox can be minimized to allow more pixels for displaying data
  • Zoom tools redesign:
    • The zoom tools have been re-organized and placed closer to the data
    • zoom slider shows the present zoom level and can be used to adjust zoom
      • Detailed zoom is a new feature that allows zooming in and out in very small increments by dragging the zoom slider and moving the cursor above it. An expert feature for e.g. large tracks.

    • New zoom tools. Easy adjustment of zoom speed for improved zooming of huge sequences.

    • Detachable Side Panel editors. A Side Panel editor can be dragged from the main workbench window and dropped outside the workbench, making a separate window e.g. on a second screen, if available.

  • Copying data in the Navigation Area runs much faster and uses less memory than before. 
  • Advanced table filter now includes an option to search for "starts with" in addition to just "contains"
  • Limitations on export of Excel 2010 files (xlsx) are removed:
    • Multiple tables can be exported to one xlsx file
    • Reports can be exported to xlsx
    • Hyperlinks are preserved in xlsx files
  • Folder contents view: subfolders will display how many items they have
  • REBASE restriction enzyme list updated to version 310.


Bug fixes

  • When translating to protein, ambiguous nucleotides potentially resulting in stop codons were not translated properly, and only the codons resulting in an amino acid were represented in the protein. Now the stop codons are also represented by an X in the protein sequence.
  • When using the “Find Open Reading Frame” tool, the input sequence was reported incorrectly in the ORF table. This has been fixed.
  • Fixed problems with Excel export that failed when special characters were used in the name.

CLC Sequence Viewer 6.7.1

Release date: September 5, 2012

Bug fixes

  • Various bug fixes

Old Releases

You can view older releases in our CLC Sequence Viewer release archive.