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Latest improvements in CLC Sequence Viewer

CLC Sequence Viewer 7.7.1

Release date: September 15, 2016

New features and improvements

  • All NCBI server communication is now encrypted. (NCBI will be moving all web services to the HTTPS protocol on September 30, 2016). 

  • The list of enzymes pre-installed in the workbench has been updated from REBASE.

  • The Quick Launch tool is now found under the Toolbox menu instead of the View menu and a button called Launch that brings up this tool has been added to the toolbar.

  • The option "is not in list" has been introduced as a new table filtering option.
  • The "Sort folder" tool now uses numerical sorting for filenames prefixed with a number.

  • New placeholders are available when defining the names of exporter outputs:  {user}, {host}, and for elements of the timestamp of the output object, {year}, {month}, {day}, {hour, {minute}, {second}. 
  • Placeholders within export output names that were previously available only as digits can now be specified using written names: {input} is a synonym for {1}, {extension} is a synonym for {2} and {counter} is a synonym for {3}.
  • GenBank import now also allows for file names with 'GBFF' extension.

  • Read group details are now shown on the Element Info view of sequence lists.

Bug fixes

  • Fixed a rare issue where some annotations could, but did not necessarily, go missing on  sequences with greater than 1000 annotations of a given type on that sequence before the deletion and where the right-click context menu option "Delete selection" was used. 

  • Fixed a bug in the "Manage Enzymes" wizard that prevented a user from cancelling the action if "Save as new enzyme list" was enabled.

  • Fixed an issue with the Import Metadata tool where, if a spreadsheet had already been loaded, then selecting the same spreadsheet again did not reload the spreadsheet content.

  • Fixed an issue where it took a long time to open a workbench it it was previouslyclosed when displaying an open table editor that had been sorted. 

  • Fixed an issue where right-clicking on a graph in a report and choosing to show "Report", "History" or "Element Info" triggered an error.

  • Various minor bugfixes.

CLC Sequence Viewer 7.7

Release date: March 31, 2016

New features and  improvements


  • All Excel sheets in a document are now imported and each sheet has a table created for its contents.
  • The CSV, HTML and Excel table/tabular exporter now use "Inf" and "NaN" values to replace the ambiguous "?".
  • In the wizard for exporting a table in CSV format, when not exporting all columns, it is now possible to cancel or go back to the previous step while selected columns are loading. 
  • An option has been added to allow the same print settings to be applied to all reports being exported to pdf format in a given export run. 
  • The "Manage Resources" tab has been removed from the the Plugin Manager.


  • Versions of individual tools are now reported in the history of output objects.
  • Export to clc format now truncates very long filenames.
  • RPM package installers for Linux are no longer available.
  • The 'Database Fields' label shown in the 'Show Element Info' view has been renamed to ' Local Attribute Fields'.
  • The user can no longer uncheck "export all columns" for input objects that do not support this option. This applies to command line functionality as well, where the user will now receive an error if this is attempted.

Bug fixes

  • Fixed a frame offset bug that occurred when translating reverse complemented CDS regions into protein sequences.
  • The "Search for sequences at NCBI" tool would in some cases fail to download nucleotide sequences with the error message "The following sequences were not downloaded correctly: ...".
  • Fixed a bug that caused the Excel importer to use column names as cell values of the first row.
  • Fixed an issue where open tabs were not correctly ordered after splitting view horizontally or vertically using the View menu or keyboard shortcuts.
  • Fixed an issue so that double clicking on clc:// urls on Mac OS X now opens the data element in a view in an installed CLC Workbench.          
  • A Workbench Data Location pointing at a file on the system instead of a folder will now appear as unavailable in the Workbench Navigation area instead of throwing an error. 
  • Fixed a bug where it was possible to type non-number characters into a number field when starting up a job in the Workbench.
  • An error was previously thrown when encountering blank annotation-values. Blank values are now ignored.
  • Fixed an error that could appear when moving the mouse over annotations in a sequence annotation table.
  • Fix an issue that could lead to an error when a job status description changed while a full description was being generated.
  • Fixed an issue where, when the option to "Skip these updates" was checked in the plugin update information window, this information was not saved. This led to the same plugin update information being presented after each Workbench restart if the plugins were not updated. 
  • Fixed an error that occurred when pressing the Print button in the Help dialog (Mac OS X only).
  • Fixed an issue where the text area in error dialogs did not expand vertically when the dialog was expanded.
  • Fixed a rare issue that could be triggered by switching editor view with a double click.

Plugin updates and fixes

All plugins need to installed in the new Workbench for compatibility reasons.

Changes to freely available plugins
  • Batch rename: Fixed an issue where a warning was displayed for entries not modified.

CLC Sequence Viewer 7.6.1

Release date: September 8, 2015

New features and improvements

  • Tooltips on leaves of phylogenetic trees now display a description of the attached sequence.
  • One can now select "EST" as database when using the Search for Sequences at NCBI tool.
  • The output of the Reverse Complement Sequence now gets the suffix -RC attached to the name of the input instead of -1 before.
  • 3D molecule viewer improvements:
    • Molecular surfaces can now be transparent
    • A clipping plane can cut into surfaces and secondary structure
    • Options for creating atom groups and visualizing hydrogen bonds have been improved

Bug fixes

  • Fixed an issue where some filtering operations, such as "doesn't contain" did not act correctly when filtering table cells that contained multiple pieces of information.
  • Fixed an issue where annotations that spanned the ends of a circular sequence would be incorrectly placed in the Circular Sequence View.
  • Fixed a bug that caused the workbench to freeze if certain sequences were displayed in circular view with radial rendering of labels.
  • Fixed an issue where some filtering operations, such as "doesn't contain" did not act correctly when filtering table cells that contained multiple pieces of information.
  • Fixed an issue that prevented a root folder on Windows drives from being used as a File Location.
  • Fixed an issue where updating an existing installation on Windows would result in the .vmoptions file being deleted, which makes the Workbench run with the default Java configuration.

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 7.0.2

Release date: March 18, 2014

Bug fixes

  • Fixed problems causing an error when trying to uninstall plugins.
  • Fixed issue with pausing and resuming running processes

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 6.9.1

Release date: October 21, 2013


  • When importing Genbank nucleotide sequences, the Workbench will determine whether it is DNA or RNA based on the sequence rather than the description in the file.

Bug fixes

  • Fixed: GFF export failed.
  • Fixed: Copying information from the Folder Contents view did not work.

CLC Sequence Viewer 6.9

Release date: August 21, 2013

New features

  • Export framework redesigned
    • Export of multiple files: you can export several files in one go. The naming of the file will default to the name used in the Navigation Area of the Workbench, but the user can specify a naming pattern to use instead.
    • Export formats: A new column “Exports selected” has been added to the “Select exporter” table that indicates with a “Yes”, “No” or “Partly” whether the currently selected element can be exported with the given exporters. Partly means that you have made a selection of elements where only some of them can be exported by the selected exporter.

    • Improved usability with a quick-select dialog for choosing the right export format. The dialog includes a  description of each exporter that can be quickly filtered.
    • Export can be integrated into workflows
    • Support for direct compression of exported files in zip and gzip.
  •  The folder view has been improved with the following:
    • It is now possible to drag and drop objects from the folder editor. This will create a copy of the objects at the selected destination.
    • Attribute columns will be left empty if the attribute has not been defined (previously attribute values that had not been defined were set to 0 and checkboxes were shown as unchecked).
    • A new column showing the first 50 residues of each sequence has been added as an option.
    • The column with the name “Length” has been renamed to “Size”.
    • The column “Size” shows the length of a sequence, or for sequence lists, the number of sequences e.g.:
      • Alignments: the length of the alignment
  • The Side Panel “Save/Restore Settings” function has been expanded with a new feature:
    • The “Save/Restore Settings” function (found at the top of the Side Panel) has been redesigned. It is now possible to save settings in two different ways. 1) The settings can be saved for this element type in general, e.g. for a track it would be save settings “For Track View in General”. In this way the settings will be applied each time you open an element of the same type, which in this case means each time one of the saved tracks are opened from the Navigation Area, these settings will be applied. These “general” settings are user specific and will not be saved with or exported with the element. 2) Settings can be saved with the specific element only e.g. for a track it would be save settings “On This Track Only”. The settings are saved with only this element (and will be exported with the element if you later select to export the element to another destination).

  • Alignments: If you have one particular sequence that you would like to use as a reference sequence, it can be useful to move this to the top. This can now be done automatically by right clicking on the sequence name and then selecting “Move Sequence to Top ”.

  • The Sequence List Table has been improved with a new feature. A new column showing the first 50 residues of each sequence has been added as an option.


  • When using the “Translate to protein ” tool, the max limit has been raised to 1GB.
  • The sequence action "Open Copy" has been removed and "Open This Sequence" has been renamed to "Open Sequence ".

  • Renaming of data in the Navigation Area by clicking twice has been improved. Previously, you could accidentally enter rename mode when the intention was to get focus in the Navigation Area. Now, you can only trigger rename by clicking when the Navigator has focus.
  • The alignment tool is now more memory efficient.
  • Tables: Improved auto-adjustment of the column width (based on content and number of columns).
  • Usability improvement of simple table filtering :
    • A dedicated filter button has been added to apply the filter directly without having to wait until the filter is automatically applied
    • For tables with more than 10000 rows, the filter will not be applied automatically after a delay. Instead, there is a helping text asking the user to apply the filter through the "Filter" button. This avoids premature filtering before entry of the filter text has completed. Since filter can take some seconds for large tables, this used to be an annoyance because the user would have to wait until filtering was done to complete the entry.

Bug fixes

  • PDF export of the history of a result did not include the name and version number of the Workbench that produced the result.


  • System requirements for Linux has changed. From this release, SuSE is supported from version 10.2. This was previously version 10.0

CLC Sequence Viewer 6.8.2

Release date: March 19, 2013


  • For alignments, sequence lists and other sequence views, the right-click options to Open Copy of Sequence and Open This Sequence have been merged to Open Sequence. If a copy should be created, use Save As with the new sequence, or drag it into a folder in the Navigation Area.

Bug fixes

CLC Sequence Viewer 6.8.1

Release date: January 23, 2013


  • Added Legal and Tabloid formats for printing

Bug fixes

  • Fixed an error when translating DNA to protein. When more than 10 sequences were produced, the resulting protein sequence included X instead of * as stop symbol. We advice customers to re-run any analyses with the translation tool when using more than 10 sequences as input.
  • Various minor bug-fixes

CLC Sequence Viewer 6.8

Release date: January 8, 2013

New features

  • Toolbox improvements:
    • New Favorite Toolbox: A new tab next to the Toolbox holds
      • Frequently used tools. This is automatically updated based on which tools are used most frequently.
      • Favorite tools: Right-clicking a tool in the Toolbox allows you to add a tool to your favorites list.
    • Quick launch of tools: Pressing Ctrl + Shift + T shows a dialog for easy typing and launching tools.
  • Relevant view settings are now copied when switching between different views of the same data. As an example: if you have specified a set of restriction enzymes to display in the circular view of a sequence and switch to the linear view, these enzymes will also be listed in the Side Panel here. Note that the Side Panel settings are only copied to the new view if they have been changed by the user in the old view.
  • Performance when sorting of large tables has been improved
  • Rename can now be done through right-click menu in Navigation Area.
  • Annotations on circular sequences:
    • When shown in linear view they have a cleaner appearance. Before, there was a line from beginning to end of the annotation, and this has now been removed.
    • When shown in circular view, it is no longer displayed as a joined annotation over the start point but as a continuous annotation.
  • Alignments: The performance of the algorithm for running multiple alignments has been improved and now runs on multiple cores.
  • Find Open Reading Frames can be run in batch and workflows
  • Translate to protein can be run in batch and workflows
  • Restriction map: Excel export now creates a sheet for both the cut sites table and the restriction map.
  • Export now has progress and can be canceled.
  • Shortcut key for Translate to Protein has changed from Ctrl + Shift + T into Ctrl + Shift + P.
  • Bug fixes

    • Fixed problem of not correctly formatting qualifiers in EMBL export.
    • Fixed a problem sorting sequence lists on modification date.
    • Various bug fixes.

CLC Sequence Viewer 6.7.1

Release date: September 5, 2012

Bug fixes

  • Various bug fixes

CLC Sequence Viewer 6.7

Release date: August 9, 2012


  • It is possible to create sequence lists based on other sequence lists (not only single sequences)
  • Listing folder elements in the Navigation Area is faster
  • Translate to protein creates sequence lists when there are more than ten sequences
  • A new translation table added: Pterobranchia mitochondrial (see

CLC Sequence Viewer 6.6.2

Release date: April 11, 2012


  • Aligned fasta import and export is now supported (see A consequence of this is that the standard fasta import of sequences will reject to import sequences that contain gaps, assuming they should be imported as alignments instead.

CLC Sequence Viewer 6.6.1

Release date: February 23, 2012


  • Translate to protein creates sequence lists as results when more than 10 sequences are produced. This greatly improves performance when translating large amounts of proteins
  • It is now possible to specify the number formatting in tables in the View Preferences.

Bug fixes

  • Fixed: Downloading of protein sequences from NCBI fails.
  • Fixed: Opening external files (e.g. pdf files or Word documents) with spaces in the file name does not work on Windows.

Old Releases

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