Latest improvements for CLC Sequence Viewer

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CLC Sequence Viewer 6.8.2

Release date: 2013-03-19


  • 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: 2013-01-23


  • 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: 2013-01-08

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: 2012-09-05

Bug fixes

  • Various bug fixes

CLC Sequence Viewer 6.7

Release date: 2012-08-09


  • 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: 2012-04-11


  • 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: 2012-02-23


  • 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.

CLC Sequence Viewer 6.5.4

Release date: 2011-11-29

New and improved features

  • Exporting fastq format no longer includes redundant name of the read in the quality score line. Now the name only appears once per read.

Bug fixes

  • Fixed: Annotations spanning the sequence from start to end did not display right when the sequence was wrapped. The annotation was only displayed on the first line.

CLC Sequence Viewer 6.5.3

Release date: 2011-10-12

New and improved features
  • Clean-up of the Workbench window so that it no longer holds information about which Workspace is active. This information is now displayed with check boxes in the Workspace menu.
Bug fixes
  • Fixed: For circular molecules, the Find Open Reading Frames tool did not find reading frames on the negative strand. We recommend users to rerun any reading frame analyses on circular molecules.
  • Fixed: Certain annotation types were mapped to generic annotation types when exporting sequences in Genbank format.

CLC Sequence Viewer 6.5.1

Release date: 2011-02-18

Bug fixes

  • Improved support for Mac OS X systems with japanese language
  • Improved support for systems with 512 MB of memory or less

CLC Sequence Viewer 6.5

Release date: 2011-01-26

New features:

  • Improved layout of restriction site annotations
    • Linear view: There is a new option for displaying labels as “Stacked” which means that the labels of overlapping cut sites can be discriminated. Read more.
    • Circular view: There is a “Radial” option that will place restriction sites (and annotations) as close to the sequence as possible with a radial layout. Read more.
  • Improved layout of general annotations
    • Linear view: There is an option to separate restriction sites and annotations in separate layers.
    • Circular view: There is a “Radial” option that will place annotations (and restriction sites) as close to the sequence as possible with a radial layout.
  • Annotation table now available for sequence lists and alignments. Read more.
  • Support for exporting tables as tab-delimited files.
  • Audit option: manual editing of sequences will be recorded with an annotation on the sequence (this has to be switched on in the Preferences dialog). Read more.
  • The default database of restriction enzymes can be expanded (requires manual edit of database file). Read more.
  • Improved option to export and import Side Panel settings. Read more.
  • Memory allocation: the default memory allocation for the Workbench changes from 75% to 50% of available physical memory with a maximum at 50 GB.

Bug fixes

  • The molecular weight calculation for the sequence statistics report is more accurate and is now reported for both single- and double-stranded molecules.
  • Various bug-fixes

CLC Sequence Viewer 6.4

Release date: 2010-06-15

New features:

  • Improved memory management in general: lower memory footprint and shorter management overhead pauses.
  • Improved memory handling of large tabular data sets.
  • Improved consistency of data handling including faster listing of folder contents
  • Performance when saving small files significantly improved
  • Sequence annotations are packed to lower memory footprint and disk space usage, especially for SNP, DIP, and Conflict annotations.
  • Improved performance of reading data files from shared drives.
  • Folder structure (expanded/collapsed folders) is preserved through the life-time of a wizard (e.g. when selecting input data and reference for read mapping)
  • Find in Side Panel: separators are allowed when performing position search (e.g. 1.000.000 or 1,000,000 or 1’000’000 or 1 000 000). Read more


  • Print of folder content now takes settings in the Side Panel into account
  • Find in Side Panel: space are now allowed
  • Genbank import: sequence name (LOCUS) was truncated to 18 characters

CLC Sequence Viewer 6.3

Release date: 2009-12-15

New features

  • Deployment
    • You can set a path to the default data location used when the Workbench starts for the first time. This is a feature to help system administrators control where new installations per default save their data. Read more…
    • Support for removing tools accessing the internet (NCBI search, update notifications etc). Read more…
  • General import and export
  • Export tables and reports in Excel format.
  • Import section of user manual re-structured to provide better overview. Read more…. Expression data importers are now described in technical details in a separate section. Read more….
  • You can now export multiple sequence lists in fasta format
  • Forced import of zip files is now supported (it will force import the contents of the zip file)
  • The standard import now accepts gzip and tar files as well as zip
  • If a forced import fails, there will be more technical information about what went wrong, allowing you to identify bad formatting of the import files
  • Both Genbank and gff importer now makes several attempts at naming genes that do not have a gene name. It will iteratively try the following qualifiers: “product”, “locus_tag”, “protein_id” and “transcript_id”
  • When importing genbank files where the length stated does not match the actual sequence, a warning is shown but the sequence is accepted.
  • When exporting in csv format, the Locale settings are used to determine whether comma or semi-colons should be used as delimiter (comma used for US locales)
  • Miscellaneous
    • Improved reporting of situations when a full disk prevents saving of data
    • Downloading sequences using drag and drop from the search table no longer creates a “Downloading…” node in the folder. The download process can be monitored in the Processes tab.
    • Extract Sequences moved from File menu to Toolbox-> General Sequence Analysis. Read more…
    • Better progress feedback on various dialogs


  • Fixed problem displaying the “Copying…” label when copying data and then updating the folder
  • Fixed problem with naming of tabs. The fix means that on Windows and Linux unsaved data now gets a * rather than make the tab name bold and italics. (This has always been the behavior on Mac OS X).

CLC Sequence Viewer 6.2.0

Release date: 2009-08-18

New features:

  • Import list of sequences in csv format: each line in the file represents a sequence with name, optional description, and sequence. Typically useful for importing lists of oligos.
  • Advanced view of elements in a folder including batch editing.
  • Extract sequences improvements
  • You can now drag results from NCBI searches into the view area to open directly (previously you could only drag into a folder to save)
  • “Find” in text view now accepts Enter as command to find the next hit
  • Importing VectorNTI archives previously resulted in a sequence list. Now it imports as single sequences.
  • Export of annotations in GFF format (note that annotations with joined regions are not supported)

Bug fixes:

  • Problem rendering scatter plots without lines
  • DNA strider files could loose name upon import
  • Rare misplacement of annotations when editing very large sequences
  • Various bug-fixes
This update is recommended for all users.

CLC Sequence Viewer 6.1

Release date: 2009-06-02

June 2, 2009

New features:

  • Better feedback on processes: there is a tool tip showing details and start time.
  • Much improved memory performance and processing time of large data sets
  • Output and error log files are now placed in the application data directory in the user home

Bug fixes:

  • Fixed error when parsing files from Clone Manager (cm5-files)

CLC Sequence Viewer 6.0.2

Release date: 2009-03-12


  • Better performance of files with many annotations
  • Fixed error and improved performance of Join Sequences tool
  • Various bug fixes

CLC Sequence Viewer 6.0.1

Release date: 2009-01-28

Bug fixes

  • Find in the Side Panel did not support spaces when searching for annotations
  • Fixed error when exporting alignments in aln format

CLC Sequence Viewer 6.0

Release date: 2009-01-28

Improved user experience of processes

  • Non-modal feedback from processes:
    • When there is a message
    • If you have chosen to save the results in the last step of the wizard, you will be notified when the process is done.
    • Processes running on the CLC Science Server will notify when they are done.
  • Possibility to open results by clicking the button next to the process
  • Possibility to find and select results in the Navigation Area by clicking the button next to the process
  • You can see a log of your process by clicking the button next to the process (even if you did not choose to see the log in the last step of the wizard)

General improvements

  • Tables:
    • New advanced filter to use numerical data for filtering and to combined several filter criteria. Click the small button next to the normal filter to see the advanced filter.
    • Visual feedback when sorting and filtering tables
    • Improved automatic detection of column width
  • Performance of graphs and plots improved
  • More elaborate error reports including error logs
  • You can specify which folder the Workbench should use for temporary files
  • Extract sequences from a sequence list, contig or alignment by right-clicking the white empty space. You will then be able to extract the sequences into a list or as separate sequences.
  • The “Find” option in the Side Panel of sequence views automatically detects if you have entered a position instead of a sequence.

Bug fixes

  • Locale settings were not automatically set right on the first start-up. The locale settings determine whether . or , should be used for before decimals. For new installations of the Workbench, it will now be set to the locale of the computer’s operating system. For existing installations, you will have to change this in the Edit->Preferences dialog.
  • Various performance improvements and bug fixes

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