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QIAGEN CLC Main Workbench 7.9.3

Release date: 2018-12-06


  • NCBI API keys for E-utilities can now be entered under Preferences | Advanced | NCBI API Key. This may be of particular interest where multiple machines with QIAGEN CLC Workbenches installed use the same IP address. If an NCBI API key is provided, it is used when running the following tools: Search for Sequences at NCBI, Search for PDB Structures at NCBI.
  • The Search for Sequences in Uniprot tool now uses the HTTPS protocol.
  • Fixed the links to the AmiGO Gene Ontology website used for GO annotations.

Bug fixes

  • Links to the HGNC (HUGO Genome Nomenclature Consortium) website are now working again.
  • Weblinks to UniProt sequences are now working again.
  • Fixed an issue where domain annotations added by the Pfam Domain Search tool started one amino acid later than expected. The corresponding start position in the table produced by the tool was correct.

Advanced notice

Only 64 bit versions of the QIAGEN CLC Main Workbench are available for QIAGEN CLC Main Workbench 8.1, released November 28, 2018, and above.

QIAGEN CLC Main Workbench 7.9.2

Release date: 2017-12-05

  • Improved the information about what to do to when a workflow needs to be updated.
  • Various minor bugfix.

QIAGEN CLC Main Workbench 7.9.1

Release date: 2017-06-22

Bug fixes

  • Fixed an issue with the Cloning tool introduced in the QIAGEN CLC Main Workbench 7.9 where the tool could not be launched.

QIAGEN CLC Main Workbench 7.9.0

Release date: 2017-06-15

New features

  • Added keyboard shortcuts to change editor views. Ctrl + Shift + PageUp and Ctrl + Shift + PageDown now changes the current view of the currently focused editor.
  • New keyboard shortcuts are available for navigation within the workbench:
    • Navigate between open tabs with Ctrl + Page Down and Ctrl + Page Up (Windows/Linux/Mac). On laptops without Page Up/Down keys, the shortcuts are Ctrl+fn+arrow up/down.
    • Return focus to the navigation area with Alt + Home.
  • We have made the following improvements to tab presentation in the View area of the Workbench:
    • Tabs show more of the name of the opened object.
    • Tabs now open from the top left corner to the right and down.
    • Tabs always stay in the same position when another tab is selected or a new tab is opened.
    • A new sub menu has been added to the right click menu on tabs to select between the open tabs.
  • Anonymous Workbench usage information can now be shared with us to help us improve our products and offerings. Information about what is collected and how to opt out is provided when the updated Workbench is launched. Further details areavailable in the manual.


  • New and improved Save View Settings dialog. This new dialog can be used for saving, applying, importing and exporting side panel views.
  • Opening large pairwise comparisons generated by the the Create Pairwise Comparison tool is now faster.

Bug fixes

  • Fixed an issue where the GFF3 Exporter could generate invalid GFF3 for features of length 0.
  • Fixed a rare issue that could cause GenBank export to fail.
  • Fixed an issue with the Realign Selection tool where clicking on the ? button to see the manual information resulted in an error. This tool is launched from the right-click context menu for selections in sequence alignments.
  • Fixed an issue where workflows run in batch mode would fail in the case where no results are saved to the Navigation Area and only one file is exported per batch unit.
  • Fixed an issue introduced in QIAGEN CLC Main Workbench 7.8.1 where the Download Sequences from NCBI tool would continue to indicate it was searching when in fact the search had finished and no items were found.

QIAGEN CLC Main Workbench 7.8.1

Release date: 2017-03-15

Bug fixes

  • Fixed an issue where the Search for Sequences at NCBI tool did not display the first and last search result in each page of results returned.

QIAGEN CLC Main Workbench 7.8

Release date: 2017-03-02


The list of BLAST databases for use with the BLAST at NCBI tool has been updated:

  • Added “RefSeq representative genomes” database.
  • Removed “New or revised GenBank sequences (month)”. This is no longer supported by the NCBI.
  • Changed “References mRNA sequences”name to “References RNA sequences”. The database that is searched remains the same as before.
  • Changed “16S ribosomal RNA sequences” database to now search the  “rRNA_typestrains/prokaryotic_16S_ribosomal_RNA” database, as listed on the NCBI website. It previously queried “TL/16S_ribosomal_RNA_Bacteria_and_Archaea”.
  • Fixed “Human genomic plus transcripts” and “Mouse genomic plus transcripts” databases configuration to reflect their new location. Searching these previously returned an error.
  • Usability aspects of data association using the Import Metadata tool have been improved, including adding a preview of data items to be associated with particular metadata rows.
  • The speed of searches for data elements with associations to specified metadata, from within a Metadata Table, has been greatly improved. To enable metadata related searches to work after upgrading to the QIAGEN CLC Main Workbench 7.8, indices for the locations containing the relevant data will need to be rebuilt.
  • A preview of data items that will be associated with particular metadata rows has been added to the Import Metadata tool.
  • Various small usability improvements have been made to the Import Metadata tool.

New features and improvements

  • Tutorial windows are no longer blocked when a wizard is open.
  • An exporter has been added to export annotations on sequences or tracks to Generic Feature Format Version 3 (GFF3) format.
  • When working with Gene Sets that refer to Gene Ontology terms, gene annotations are now automatically propagated to parent Gene Ontology terms. This improvement affects the tools Hypergeometric Tests on Annotations and Gene Set Enrichment Analysis (GSEA).
  • It is now possible to right-click on a table cell and filter table rows based on the value of that cell by choosing options under the new context menu section called  "Table filters". This change applies to all tables where advanced filtering is available.
  • Support has been added for 'negative lookahead' when using Java regular expressions when using the Motif Search Tool.
  • In cases where tools within a workflow have been renamed, it is now possible to filter for original tool names within the workflow configuration view of the workflow editing tool.
  • Various minor improvements

Bug fixes

  • Fixed an issue with GenBank and EMBL exports where quoting specifications were not being conformed to.
  • Fixed an issue where a workflow containing an export step that failed did not provide any indication that a problem had occurred.
  • Fixed an issue with the Annotation Table view of a sequence where it was possible to change the types of annotations displayed at the same time as an annotation was being edited, which could lead to an error being thrown or the wrong annotation being changed.
  • Fixed an issue with Primer Tables where an error resulted if either the option "Save Primer(s) Fwd, Rev" or "Save Fragment" was chosen and then the save operation was stopped by clicking on the Cancel button.
  • Fixed an issue where in some cases filtering tables for empty values would not produce any results.
  • Fixed an issue where advanced filtering did not work when looking for rows with cells containing multiple values using the filtering term "=" (equals).
  • A sporadic java issue that led to errors including the text "java.lang.ClassCastException: sun.awt.image.BufImgSurfaceData cannot be cast to sun.java2d.xr.XRSurfaceData", has been addressed through an upgrade to java. This issue was primarily seen when using the Workbench remotely on Linux systems.
  • Fixed a problem with the identification of the correct sequence types from MLST schemes in cases where the schemes contained blank characters. This issue affected workbenches with CLC MLST installed.
  • Various minor bugfixes.


  • The GFF exporter has been retired and is no longer available. The new GFF3 exporter should be used instead.

Other notifications

  • An option to opt out of providing anonymous usage information to QIAGEN has been added to the Workbench Preferences. We are not yet collecting any usage information so opting in or out does not have any effect at this time.

QIAGEN CLC Main Workbench 7.7.4

Release date: 2017-06-08

Bug fixes

  • Fixed a problem with the identification of the correct sequence types from MLST schemes in cases where the schemes contained blank characters. This issue affected Workbenches with the CLC MLST Module installed.

QIAGEN CLC Main Workbench 7.6.7

Release date: 2017-03-22

All changes in this release have also been fixed on the QIAGEN CLC Main Workbench 7.8.x and 7.7.x lines at time of writing, with the exception of the one release note marked with an asterisk. That issue was fixed for QIAGEN CLC Main Workbench 7.8.0 and will be fixed in future in the QIAGEN CLC Main Workbench 7.7.x line.


  • All NCBI server communication is now encrypted (uses HTTPS).
  • Updated the URL to use for links to UniProt databases.
  • Updated BLAST executables to be compatible with macOS Sierra. This change only affects Mac users.

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 a problem with the identification of the correct sequence types from MLST schemes in cases where the schemes contained blank characters. This issue affected workbenches with CLC MLST Module installed.*

QIAGEN CLC Main Workbench 6.7.2

Release date: 2012-12-07

Bug fixes

  • Fix to the proxy settings recognition meaning that download of BLAST databases now works when there is a proxy setup.
  • Fixed problem of not correctly formatting qualifiers in EMBL export.
  • Fixed a problem sorting sequence lists on modification date.
  • Test on proportions: Fixed an error caused by the wrong group being used as reference, which means that the positive values should have been negative and vice versa.
  • Various bug fixes.

QIAGEN CLC Main Workbench 6.7.1

Release date: 2012-09-05

Bug fixes

  • Fixed: Workflows would fail when intermediate results were empty (e.g. if no variants were found and a variant track was used for subsequent analysis).
  • Various bug fixes

QIAGEN CLC Main Workbench 6.7

Release date: 2012-08-09

New features

  • Workflows can be built in the Workbench to combine various tools from the Toolbox into one analysis, connecting the output from one tool to the input from another
  • In the first release, the gateway cloning tools are the only tools that can be incorporated into workflows.
  • Workflows can be distributed and installed either in the Workbench or in the QIAGEN CLC Genomics Server
  • The creator of the workflow can configure parameters for the workflow and these will be fixed when the workflow is distributed and installed
  • The creator of the workflow decides which of the output from the tools that should be saved and which should be discarded
  • Workflows can be run in batch, making it a powerful tool for crunching high numbers of samples through the same pipeline.

Plugin updates

Grid integration plug-in is integrated into the general server plug-in. If a grid preset is present on the server, the Grid option becomes available in the Workbench dialog.

QIAGEN CLC Main Workbench 6.6.5

Release date: 2012-07-25


  • Support for Mac OS X 10.8, Mountain Lion

Bug fixes

  • Fixed: Problem with online BLAST at NCBI

QIAGEN CLC Main Workbench 6.6.2

Release date: 2012-04-11


  • Aligned fasta import and export is now supported (see http://www.bioperl.org/wiki/FASTA_multiple_alignment_format). 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.
  • The license order ID is visible in the License Manager, both for static and network licenses. For security reasons, the last 10 characters of the ID are masked. This will prevent unauthorized persons from copying the license order ID to another computer, but will allow the CLC staff to identify the license used.

Bug fixes

  • Fixed: Cloning bug: when performing restriction cloning in regions with single-stranded DNA, you would get an error.

QIAGEN CLC Main Workbench 6.6.1

Release date: 2012-02-23

New features

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.

QIAGEN CLC Main Workbench 6.6

Release date: 2012-02-13

New features

  • Printing and pdf export of assemblies: the assemblies are now wrapped to make better use of the paper.
  • Usability of Close icon on tabs has been improved. Both in terms of responsiveness and making it impossible by accident to initiate a drag and drop movement when you hit the close icon to try to close a tab.
  • "Show" submenu has been removed from File Menu, and the right-click menu now includes only the relevant views and editors. This provides a better overview.
  • The behavior of the Close Other Tabs function has changed so that it will close all views, regardless of the way the view area is split.
  • The most common annotation types are assigned a special color per default. Other annotation types previously got the same color. This has been extended so that the Workbench attempts to find a special color for each type.
  • VectorNTI import is no longer in a separate plug-in but part of the Workbench. The functionality remains unchanged.

New plug-ins and plug-in updates

  • Additional Alignments Plug-in updated
    • The algorithms have been updated to the most recent versions
    • The list of algorithms has been reduced to two for compatibility reasons

QIAGEN CLC Main Workbench 6.5

Release date: 2011-11-29

New plug-ins and plug-in updates

  • MLST module updated
    • Possible to download MLST schemes from any web site compatible with mlstDBnet
    • When a new allele is called because the sequencing reads are not long enough, this is reported in the isolate view rather than “New allele”

See a list of all plug-ins here.

New and improved features

  • Multi-site Gateway Cloning. You can perform multi-site gateway cloning and in a few clicks create your expression clones with multiple fragments. The existing Gateway Cloning tool has been expanded so that you can easily recombine several fragments as well as continue using it for the standard Gateway Cloning
  • Process tagged sequences
    • A summary report is now available with an overview of the number of reads per bar code
    • You can search for barcodes (MIDs) on both strands, supporting new 454 protocol
  • Find Binding Sites and Create Fragments improved:
    • If your template sequence contains ambiguity nucleotides (like N, Y etc), these will no longer count as mismatches when checking your primers. Note that the primer base of course need to be covered by the ambiguity symbol (e.g. a T would still be a mismatch if the template sequence has an R, which means either A or G)
    • Fixed: When using multiple template sequences, the choices to open or annotate a fragment from the fragment table did not work properly. They always applied to the first sequence although the fragment was located on another sequence (as indicated in the table)
  • 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
  • Fixed: Set-up experiment would crash when using many samples
  • Fixed: Calculation of consensus sequence in read mappings: Sometimes a majority of gaps would be ignored and a base erroneously introduced in the consensus sequence. It occurs when 1) there is no coverage in an initial segment of the reference sequence, and 2) a gap is encountered in the global read alignment. From that point onwards, gap counts are included in the consensus vote, but they are taken from the start of the mapping (where they are all 0), so they are out of sync with associated base counts. High gap counts would then kick in further downstream, possibly making the consensus a gap where it should not be. We recommend checking your mapping results manually if you rely on using the consensus sequence for further analysis
  • Fixed: importing adapters for trimming and barcodes for de-multiplexing did not work properly for CSV files and empty rows in Excel files were not allowed
  • Fixed: Motif search did not exclude regions with Ns when the option “Exclude matches in N-regions for simple motifs” was selected

QIAGEN CLC Main Workbench 6.2

Release date: 2011-10-12

New and improved features

  • You can switch between compactness levels by pressing the Alt key while scrolling with your mouse or touchpad
  • Translation in the Side Panel of nucleotide sequences now includes options to translate “All forward” or “All reverse” reading frames
  • Conflict table view of read mappings: reference positions also reported in addition to the consensus sequence position
  • Alignments: it is now possible to copy all annotations from one sequence to other sequences in the alignment
  • Cloning editor: number of restriction cut sites and motifs are shown separately for the sequence currently displayed and for all sequences in the list
  • Restriction enzymes updated with latest REBASE version
  • 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: Experiments tables can now be exported in Excel and csv formats
  • Fixed: BLAST searches at NCBI always searched nr or nt, regardless of which database was specified. This has been a problem since the release of QIAGEN CLC Main Workbench 6.0
  • Fixed: Pattern discovery wizard failed when the tool is run for the second time
  • Fixed: Certain annotation types were mapped to generic annotation types when exporting sequences in Genbank format

QIAGEN CLC Main Workbench 6.1.1

Release date: 2011-07-14

Bug fixes

  • Fixed: A cache-related bug which would sometimes result in errors when running large jobs.
  • Fixed: The UniProt search has been updated to reflect URL-changes at uniprot.org
  • Fixed: A problem with microarray experiments where large experiments could not be analyzed

QIAGEN CLC Main Workbench 6.1

Release date: 2011-06-21

New and improved features

  • All history entries will from now on include the version number of the software
  • Performance of Excel 2010 exporter improved in terms of speed and memory requirements
  • When using a license server, the Workbench user can now specify a custom user name which can be checked in the license server configuration. This makes it possible to get more fine-grained control of the users of the license server
    • BLAST parameters have been changed so that number of threads is 1 per default (there is a bug in the BLAST code provided by NCBI which makes it fails on certain data sets when using multiple threads)
    • The “Mask lower case” option has been removed
    • Tool to download BLAST databases from NCBI within the Workbench

Bug fixes

  • Fixed: Alignment-based primer design failed for columns with many gaps
  • Fixed: “Find Binding Sites and Create Fragments” did not find binding sites where the primer extended the 5′ end of the template sequence
  • Fixed: Import of certain special Genbank files failed
  • Various minor bug fixes

QIAGEN CLC Main Workbench 6.0.2

Release date: 2011-04-04

New and improved features

  • Local BLAST is faster when blasting against small databases

Bug fixes

  • Fixed: Local BLAST did not work on Mac OS 10.5
  • Fixed: Joined annotations did not get the right off set when inserting a sequence in the cloning editor
  • Fixed: Import of GO annotation files did not work
  • Various minor bug fixes

QIAGEN CLC Main Workbench 6.0.1

Release date: 2011-02-18

Bug fixes

  • Fixed issue with synonymous overhang characters in cloning editor
  • Graphics export now works with restriction sites shown
  • Gene Ontology Annotations can now be imported
  • Improved support for Mac OS X systems with japanese language
  • Improved support for systems with 512 MB of memory or less
  • Blast: Fixed issue with BLAST database creation taking too long under certain circumstances
  • Blast: Fixed issue concerning errors when input sequence names contained illegal characters
  • Blast: Fixed issue with Extract And Open option being erroneously disabled
  • Blast: Option to enter custom Entrez Query limits in Blast at NCBI re-introduced
  • Blast: Improved speed when using Blast results as input to wizards

QIAGEN CLC Main Workbench 6.0

Release date: 2011-01-26


  • Cloning tool re-designed to make it easier and faster to perform restriction cloning
    • Restriction sites used to select target vector and fragment
    • Sequences can now be displayed in circular mode in the cloning editor
    • Only one sequence displayed at a time (there is a list at the top of the view to switch between sequences)
    • Option to clone several fragments and adjust overhangs and orientation in one dialog
    • New cloning tutorial available for a quick introduction
  • BLAST tools have been redesigned
    • New Blast Database manager for easy administration and management of local BLAST databases
    • More user-friendly way of creating and accessing local BLAST databases
    • Much more stable design of both BLAST at NCBI and Local BLAST when running large data sets
    • The SNP Annotation using BLAST tool has been discontinued
    • See migration notes for using your old databases
  • 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
    • 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
  • 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
  • Motif search available in Side Panel
    • Dynamic annotations will be added for motifs defined in the Side Panel (similar to restriction sites)
    • Use motif lists to add your own motifs to the Side Panel
  • Annotation table now available for sequence lists, contigs, BLAST results and alignments
  • Batching functionality available for selected tools
  • Multiplexing: Process tagged sequencing data
    • It is now possible to import and use a file with bar codes and sample names. This makes it easier to process data with a high number of multiplexed samples
    • You can specify separate output folders for each sample, making it convenient to batch process the subsequent analyses
  • 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)
  • The default database of restriction enzymes can be expanded (requires manual edit of database file)
  • The default set of codon frequencies can be expanded (requires manual edit of table files)
  • Improved option to export and import Side Panel settings
  • 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

QIAGEN CLC Main Workbench 5.7.1

Release date: 2010-08-19


  • Improved performance of table filtering. Removed limit on the number of rows that can be filtered.
  • Option to search for read names in contigs (and also sequence lists and BLAST results).
  • Improved performance of conflict table view of contigs.
  • Better layout of graphics export and printing of contigs results: reference and consensus sequence repeated to provide an orientation context on all pages.


  • Fixed error when opening tables generated by the Transfac plug-in and the primer search tool
  • Fixed problem updating preview in Gateway cloning dialog
  • Genbank export of annotations on the negative strand were not in the right order
  • Fixed problems regarding editing and viewing of contigs and alignments
  • Fixed memory and performance issues related to import of many sequences, eg. from ACE files.
  • Various minor bug fixes

QIAGEN CLC Main Workbench 5.7

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
  • Performance of ACE export improved, especially for long reference sequences or read mapping tables.
  • 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.
  • REBASE collection of enzymes updated to latest version
  • BLAST: In the overview BLAST table, it is now possible to extract query sequences. Read more
  • Process tagged sequences: it is now possible to input barcodes on a comma-separated list. Read more
  • 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
  • Normalization of expression data: it is now possible to do “Reads per 1,000,000″-style normalization of count-based data. Read more
  • New preference group called “Data” to hold information about adapter sequences and Gateway cloning primer additions. Read more


  • Print of folder content now takes settings in the Side Panel into account
  • Process tagged sequences of paired data: it was not possible to specify one read without sequence (necessary for Illumina barcodes using paired data)
  • Better memory handling in conflict table
  • Find in Side Panel: space are now allowed
  • Genbank import: sequence name (LOCUS) was truncated to 18 characters

QIAGEN CLC Main Workbench 5.6.1

Release date: 2010-02-04

Bug fixes

  • Fixed error concerning naming of dots in PCA plot
  • Error in folder editor that prevented all elements to be shown is fixed.
  • Documentation on trim using quality scores has been updated
  • Fixed error preventing manual editing of contigs under special circumstances
  • Various bug fixes

QIAGEN CLC Main Workbench 5.6

Release date: 2009-12-15

New features

  • Expression analysis:
    • Volcano plots: you can now choose the values to plot on the x-axis. Choose between “Difference” and “Fold change”. Read more…
    • Table view of bar plots shows the same intervals as are shown in the bar plot.
    • Generic importer for expression array data in tabular format. Read more…
    • Generic importer for expression experiment annotation data in tabular format. Read more…
    • Gene Ontology (GO) files can now be used to annotate an expression experiment. Read more…
    • Tag profiling: You are no longer allowed to annotate tag samples, only experiments
    • Side panel of experiment table has been re-organized to provide better overview. Read more…
  • Opening consensus sequence including gaps will also put Ns before the consensus sequence starts and after it ends
  • 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 BLAST, update notifications etc). Read more…
  • General import and export
    • Support for import of complex regions from GFF files
    • 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)
    • GFF plug-in has been updated to accept complex annotations
  • Miscellaneous
    • Advanced retyping of annotations using the annotation table. Read more…
    • 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.
    • Primer design now supports PCR fragments longer than 5000 bp.
    • Extract Sequences moved from File manu 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).

QIAGEN CLC Main Workbench 5.5

Release date: 2009-10-08

New features

  • Gateway cloning. Simple and easy-to-use support for creating Gateway entry and expression clones.
  • Search for matches among all your saved primers. The Find Binding Sites tool has been greatly improved to now allow you to search among all your primers. In addition, you also get a tabular output of the binding sites and possible fragments.
  • In silico PCR: create PCR product based on primer pair and template sequence (including primer extensions). As part of the improved Find Binding Sites and Create Fragments tool, you can extract the PCR product from the list of fragments through a right-click menu.
  • Check primer specificity. As part of the improved Find Binding Sites and Create Fragments tool, you can search with a primer pair in a list of potential target sequences and see an overview table of binding sites and mismatches as well as potential PCR fragments.

Bug fixes

  • Various bug fixes

QIAGEN CLC Main Workbench 5.2.0

Release date: 2009-08-18

New features

  • Create new contig from selection
  • 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.
  • Heat maps and clustering improved:
  • Annotating samples or experiments for expression analysis:
  • Microarray import improved:Added support for import of more versions of native Illumina BeadChip and GEO expression files
  • 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)
  • Export of sequence data in fastq format
  • Now possible to perform detailed manual editing of contigs with up to 100,000 reads
  • Improved performance when zooming large contigs displaying a coverage graph

Bug fixes

  • Microarray import: Fixed a bug that prevented import of expression data with white spaces in column names.
  • Problem when adding annotations to an Illumina array file
  • Fixed problems importing expression annotation files
  • Fixed tblastn numbering issue
  • Fixed problem with graphics export of contigs
  • 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.

QIAGEN CLC Main Workbench 5.1

Release date: 2009-06-02

Data formats

  • Data generated with version 5.1 cannot be read in earlier versions

New features

Bug fixes

  • Fixed error when parsing files from Clone Manager (cm5-files)
  • UniProt search works again

QIAGEN CLC Main Workbench 5.0.2

Release date: 2009-03-12


  • Corrections to the ACE export
  • Better performance of files with many annotations
  • Fixed an error in RNA Structure Evaluation
  • Fixed error and improved performance of Join Sequences tool
  • Fixed error in Find Binding Sites on Sequence: no longer distinguish between lower and upper case
  • Various bug fixes

QIAGEN CLC Main Workbench 5.0.1

Release date: 2009-02-26


  • Find in the Side Panel did not support spaces when searching for annotations
  • In the cloning editor under special circumstances, an error occurred when replacing a selection with fragment
  • Sequence statistics codon count were not correct when using sequences
  • Fixed error when deleting a selected read in a contig
  • Fixed error in experiment table under certain sorting and filtering combinations
  • Fixed error when exporting alignments in aln format

QIAGEN CLC Main Workbench 5.0

Release date: 2009-01-28

New features

Expression analysis including digital gene expression
  • Support for both microarray- and sequencing-based (RNA-Seq) expression data
  • Visualization: Interactive heat map, table and scatter plot views
  • Transformation and normalization tools
  • Quality control tools including principal component analysis, MA- and boxplots
  • Experimental design tools for two- or multiple group comparisons
  • T-tests and ANOVA analysis with support for paired/repeated measures
  • Multiple testing corrected p-values (Bonferroni and/or FDR)
  • Clustering algorithms: hierarchical clustering, k-means and Partitioning Around Medoids (PAM) with support for various distance and linkage measures.
  • Ability to import NetAffx annotation arrays and adding annotation to experiments
  • Tools for Gene Set Enrichment Analysis (GSEA) and for Hyper-Geometric based tests for overrepresented annotation categories (e.g. ‘GO’stats or specific protein pathways).
  • Ability to work with Expression Arrays and RNA-seq results at the same time, enabling comparison of results
  • Right-clicking a graph (e.g. coverage) on a contig lets you export the data points to a csv file.
  • Multiplexing – Process Tagged Sequences now has an option to filter away groups with few sequences. This is an advantage if you have very ambiguous barcode definitions where sequencing errors would lead to a lot of “false” groups. These groups can now be filtered because of their small size. (The option is called “Minimum number of sequences” and is found in the third step of the wizard.)
  • Importing assemblies with more than one contig creates multi contig tables (ace and cas file import)
Improved user experience of processes
  • Non-modal feedback from processes:
    • When there is a message (e.g. from a BLAST search: not hits found)
    • 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)
3D editor re-design
  • The 3D editor now allows you to select individual structure subunits, residues, active sites, disulfide bridges and even atoms, and to customize their appearance
General improvements
  • Limited mode: when using a license server – if there are no more licenses left, you can still access your data. The Workbench will then run in Limited mode where only a few tools are available (corresponds to the tools found in CLC Sequence Viewer). Click “Limited Mode” in the license dialog.
  • 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
  • Local BLAST is upgraded to use NCBI BLAST version 2.2.19
  • 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.


  • Extract Annotations plug-in has been improved:
    • Possibility to specify the naming of the sequences (based on annotation name, type etc)
    • Performance improvements to make it possible to extract annotations of large genomes.
  • MLST plug-in: various bug fixes

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.
  • Fixed problem when BLASTing with an empty sequence
  • Various performance improvements and bug fixes

QIAGEN CLC Main Workbench 4.1.2

Release date: 2008-11-28

The following has been updated

  • The Side Panel’s Find only high-lighted the first hit. This is now fixed.
  • Local BLAST: solved problem applying command-line parameters, now a checkbox determines whether command-line options should take effect
  • BLAST: it was possible to use a BLAST result as input and database
  • Trace data: fixed an error when deleting parts of an unsaved sequence with traces
  • Better performance when zooming a dot plot
  • Better performance when using the Side Panel’s Find in large contigs and sequence lists
  • When right-clicking a CDS annotation and translating into protein, gaps were erroneously introduced into the protein sequence
  • There was an error related to selecting sequences in the Cloning editor
  • Multi-select (using Ctrl / Command key) did not work for sequence lists
  • Various bug fixes

QIAGEN CLC Main Workbench 4.1.1

Release date: 2008-10-02

The following has been updated

  • Fixed problems when scrolling very large sequences
  • Fixed problem when importing very large GenBank files
  • Improved possibilities for navigating contigs

QIAGEN CLC Main Workbench 4.1

Release date: 2008-09-18

New features

General performance improvements
  • Improved performance when handling large data sets
Import and export
  • Contigs can be exported in ACE format
  • Export of graph data points in csv format
Various high-throughput sequencing improvements
  • Possibility to open consensus sequence with gaps. Right-click the label of the consensus sequence in the contig view and select: Open Copy of Sequence Including Gaps. The gaps will be represented by Ns in the new sequence.
  • Dynamic consensus graph removed from contig view. Since contigs now have a “real” consensus sequence which is also updated to reflect changes in the reads, the dynamic consensus sequence which is switched on in the Side Panel has been removed.
  • Annotations can be transferred from reference to consensus sequence in bulk. Right-click one of the annotations and choose “Copy to Consensus Sequence” or “Copy Annotations of Type xx to Consensus Sequence”.
Plug-in updates
  • New plug-in! GFF/GTF support: You can now annotate a sequence using a GFF/GTF file. The plug-in is available for all Workbenches (not CLC Sequence Viewer). Once installed, you find it in Toolbox->General Sequence Analysis-> Annotate from GFF/GTF File. Read more…
  • Extract annotations plug-in updated: it now uses the name of the annotation as the name of the new sequence.

Bug fixes

  • Fixed bugs related to contig editing.
  • Various bug-fixes.

QIAGEN CLC Main Workbench 4.0.1

Release date: 2008-07-10

New features

  • Scrollbars can be adjusted manually

Problems fixed

  • Fixed problems when aligning sequences with lowercase characters
  • Fixed import of trace files without quality scores
  • Fixed problem when removing location
  • A new sequence list can be created from a selection in the table view
  • Better memory handling and managment of large contigs
  • User definable scrollbar areas for contig views
  • A few other minor bugs have been fixed.

QIAGEN CLC Main Workbench 4.0

Release date: 2008-06-26

Performance improvements
  • Support for data handling for larger sequence lists
  • Import of larger sequence lists (fasta)
  • View larger sequence lists
  • Sequence views with annotations are rendered much faster
Licensing system
  • More smooth system for handling licenses based on license order IDs
  • Support for download of a license via web interface
  • License server support for plug-ins
  • User-friendly license wizard
  • More reliable license system
  • Easier to upgrade to newer versions
  • Better correspondence between tables and sequence lists (e.g. selecting a row in the table high-lights the corresponding region on the relevant sequence)
  • Number of selected rows in a table is now shown in the status bar
  • Enzyme lists and restriction site tables now includes information about the length of the recognition sequence of the enzyme
  • Create a new sequence list from selected sequences in the sequence list table (right-click the selected sequences)
  • Support for copying from an enzyme list and pasting into a spreadsheet
  • Fine-grained filtering of specific columns in a table
  • Alignments: possible to batch delete sequences
  • Alignments: possible to toggle marked status of sequences
  • Shift-clicking to extend selection also works on sequences with restriction sites
  • The mouse cursor’s position on the sequence is now shown in the status bar
  • More fine-grained control when deleting annotations on multiple sequences
  • Element info replaces the old “Sequence info” view and the “Properties” window. Undo-support and support for database-specific keywords.
  • Improvement of scale layout of graphs
NCBI and UniProt search
  • Results for searches includes information about the length of the sequence
  • Ordering of search results makes it easier to add more results to the list
  • Assemble to Reference is now able to include both a consensus and a reference sequence in the same view
  • There is a limit of max of 2000 sequence that can be assembled in one run
  • Multiplexing:
    • Sort sequencing reads based on their name to facilitate batch runs
    • Sort sequences based on tag/barcode within the sequence
  • Low coverage quick-find button in the Side Panel
  • Advanced display of quality scores (colors/graph)
  • Conflict table supports large contigs
  • Coverage graph is shown per default
  • Find Inconsistency renamed to Find Conflict
  • Find Conflict treats gapped region as one conflict
  • Advanced algorithm for Maximum Likelihood inference of phylogeny.
  • ML estimation of model parameters on fixed phylogeny
  • Substitution models included:
    • Jukes Cantor
    • Kimura 80
    • HKY
    • GTR
  • Local BLAST upgrade to 2.2.18
  • NCBI BLAST uses the new server at NCBI
  • The BLAST table includes information about the overlap
  • Extract sequences works for large BLAST results, alignments, sequence lists and contigs
  • Use an imported fasta file as motif list
  • Better naming of primers when saving from primer table
  • Motif search: the table now shows information about the length of a match
  • Better correspondence between tables and sequence lists (e.g. selecting a row in the table high-lights the corresponding region on the relevant sequence)

CLC Combined Workbench 3.6.2

Release date: April 9, 2008
The following has been updated
  • A few bugs resolved caused by the MLST plug-in
  • BLAST of contigs no longer changes the contig name
  • Fixed issue with tooltip rendering of quality values on reversed sequencing reads
  • A few other minor bugs have been fixed.

CLC Combined Workbench 3.6.1

Release date: February 28, 2008
The following has been updated
  • Various bug-fixes
  • Fixed selection errors in cloning editor
  • Name of saved primers were incorrect
  • It is now possible to include NCBI BLAST in protein report
  • Fixed copy/paste errors in sequence list table
  • Made it possible to Ctrl-doubleclick to extend selection between restriction sites
  • Improved user interface for adding motifs to motif lists

CLC Combined Workbench 3.6

Release date: February 6, 2008
The following has been updated
  • Motif list search: It is now possible to do motif search using a list of motifs.
    • The list of motifs can be saved and exported
    • The list can contain different types of motifs: simple or regular expressions (Java or PROSITE)
  • Multi request NCBI BLAST (up to 50 concurrent requests)
    • Makes it much faster to BLAST multiple sequences
    • Improved status messages when BLASTing multiple sequences
  • Contigs (consensus sequence) fully supported by BLAST (both Local and NCBI)
  • Extended BLAST table:
    • Shows if the hit is on the positive or negative strand
    • For tblastn, the reading frame for the hit is shown
    • The number of gaps, and gap percentage is shown
  • BLAST overview table contains more information:
    • Shows hit with greatest percent identity
    • Shows hit with greatest percent positive
    • Shows longest hit
  • Restriction sites available in Side Panel are computed up to 6 times faster
  • Enzyme tables support “delete” via Tool bar and Delete key
  • Enzymes already present in side panel are shown in [ ] brackets in “Show Enzymes Cutting Inside/outside Selection”
  • It is now possible to reverse a sequence. Available both in the Toolbox under Nucleotide Analysis and in the right-click menu in the Cloning Editor.
  • Better focus system – it is now easier to see what part of the screen that has focus. An error in the focus system has also been corrected.
  • Various bug fixes.

CLC Combined Workbench 3.5.1

Release date: December 18, 2007
The following has been updated
  • Organism name is now available in sequence list tables
  • Fixed Mac problem when closing tabs
  • Fixed minor issues and improved overall program stability
  • Improved view layout of very long sequence labels
  • Fixed stability issues related to the Recent Items plugin
  • Improvement of a few issues regarding visualization of RNA structures on alignments

CLC Combined Workbench 3.5

Release date: December 06, 2007
  • Search
    • Full text search (quick search field)
      • Query guide system (Shift + F1 in search field)
      • Pressing Alt while clicking: locate data in Navigation Area
    • Full text search editor
      • Can be saved for quick search later on
    • Automatically updated search index of all data
  • New floating license concept
    • Automatic license server detection
    • Advanced license borrowing enables off-line use of workbench
  • New and improved plug-in and resource management
    • New user interface
    • Quick button in toolbar
    • New concept: Resources – PFAM databases can be downloaded for easy update
    • Better progress measurement during download, installation etc.
    • Automatic update check
    • Integrated plug-in registration: SignalP, TMHMM, MLST
  • Automatic restart (after plug-in installation, exceeding of memory capacity and license changes)
  • Cut, copy, paste and delete actions work better in both sequence viewers and tables (no need to right-click any more)
  • Position of annotations in alignments, contigs etc. now relative to both alignment and sequence
  • Numeric scales now shown on graphs along sequence (hydroplots, coverage, conservation, sequence logo etc)
  • Selecting a row in a table makes an interactive selection on the corresponding sequence (now implemented for all relevant tables)
  • The Find functionality in the Side Panel has been improved to make it possible to search in sequences with ambiguity character e.g. Ns
  • It is possible to open much larger sequence lists in the graphical view.
  • Significantly faster algorithm now including multi processor technology – more than 4 times faster
  • New action to reassemble contig
  • Interactive mouse-adjustment of trimmed and excluded regions of sequence reads
  • Refined conflict annotations now includes both existing and resolved conflicts
  • Possibility to trim for multiple user defined vector sequences
  • New action to reverse contig
  • New right-click action to add sequences to an existing contig
  • Sorting of contig reads (like alignments)
    • By hand (mouse)
    • By name
    • By length
    • By start position
  • Individual scaling of trace data: mouse-grab the trace graph and drag up or down
  • Possible to insert gaps in consensus sequence (Delete)
  • Import of ACE files (e.g. contigs from Phrap)
  • IUPAC codes included in the Contig table
  • Editing sequence reads dynamically updates conflict annotations on consensus sequence (state: conflict or resolved)
  • New right-click option on a consensus sequence selection: Transfer Selection to All Reads
  • Trimming is performed twice as fast
Restriction sites
  • Side Panel re-design
    • Sorting of enzymes by alphabet, number of cuts or overhang type
    • Simpler management of enzymes
    • Improved tool tips on side panel enzymes showing recognition sequence and cleavage pattern
    • Quickjump to restriction sites
  • Improved enzyme selection wizard
  • Improved action to Show Enzymes Cutting Inside/Outside Selection
    • New layout
    • Easier to understand
    • Improved filtering of enzymes cutting inside or outside the selection
    • Preview of enzymes to be added to the side panel
  • Tool tips on restriction sites now include:
    • Methylation inhibition
    • Possible star activity (non-specific recognition and cleavage)
  • Enzyme list table:
    • Information about possible star activity (non-specific recognition and cleavage)
    • New button: Add/Remove Enzymes
    • New button: Create new enzyme list from selection
  • Greatly improved wizard for in-silico cloning
    • Detailed table view of all available insert sequences
    • Interactive overhang “editor”: simple mouse interaction easily adjust sequence ends emulating exonuclease activity or Klenow fill
    • Graphically advanced compatibility aid and check of sequence ends
  • Easily find enzymes with compatible ends
  • Inserted fragments now include annotations with information about the parent sequence and the performed cloning steps
  • Common cloning vectors now included in Example Data
  • Naming of sequences in cloning editor now reflects the enzymes which have cut
  • Local “on-the-fly” BLAST (also Cube and Cell)
    • No need to build BLAST database aforehand
  • Multi BLAST table – overview when blasting multiple input sequences(also Cube and Cell, NCBI BLAST, SNP BLAST)
  • Possibility to use command line options in Local BLAST
  • Hit length is shown in table view
  • (Local) BLAST performance much improved for very large sequences
  • Partition function calculation included
    • Calculates the complete secondary structure partition function.
    • Calculates the probabilities of all possible base pairs and the probability that any single base is unpaired.
    • Creates a plot of base pair probabilities.
    • The pairing probabilities are distinguished by color codes in both the linear- and the secondary structure editors.
  • Structure scanning
    • Scan larger sequences for the existence of local stable RNA structures.
    • Creates a plot of structure formation probability. Statistical significance of a local structure can be seen as spikes in the graph.
  • Hypothesis testing
    • Testing hypotheses about an RNA structure using added structural constraints
    • Probability assigned to hypothesis using the partition function
  • Import and export of RNA secondary structures in different formats (ct / col / rnaml / xml).
    • Shuffle sequence includes more algorithms – now possible to shuffle while preserving di-nucleotide frequency
    • Added codon frequency tables for: *Arthrobacter aurescens TC1 *Streptomyces coelicolor A3(2)
    • Finding open reading frames: the table includes more information:
      • Strandedness
      • Nucleotides in the start codon
    • It is now possible to extract all sequences from a sequence list, an alignment or a contig (File->Extract Sequences)


  • Sequence reader – reads sequence aloud
  • Recent items – show updated list of recently used data
  • VNTI import – including import of VNTI archives

Example data

  • Example data is included in the installation file – no need for download
  • Large vector library included
  • New RNA sequences

CLC Combined Workbench 3.0.3

Release date: October 04, 2007
The following has been updated
  • Better import of aln files
  • Solved problem with annotation rendering when inserting long sequences
  • Annotation labels are now appended when exporting into GenBank format
  • BLAST binaries are updated to version 2.2.17 which fixes some issues on the Windows platform
  • Improved stability of the cloning editor
  • Fixed problems with unstable contig objects

CLC Combined Workbench 3.0.2

Release date: August 22, 2007
The following has been updated
  • BLAST databases are not indexed per default any more
  • More information added to the BLAST output table
  • Improvement of regular expression syntax in motif search
  • Fixed error in contig editing
  • A few help updates
  • Better detection of memory on computers with more than 2 GB RAM
  • Better license handling on Windows Vista
  • Fixed error in alignment editing
  • Improved program stability
  • Improved ORF detection on negative strands of circular molecules
  • Better file naming when importing raw sequence data

CLC Combined Workbench 3.0.1

Release date: July 5, 2007
The following has been updated
  • Better handling of PFAM databases
  • Fixed error in conversion of old sequence data with lowercase characters
  • Old data can now be converted through the help menu
  • Fixed error when trying to save an element to non-selected location
  • A few help updates
  • Better license handling on Windows Vista
  • Fixed error in alignment editing

CLC Combined Workbench 3.0

Release date: June 28, 2007
The following has been updated
  • Highlights
    • All the features of the CLC RNA Workbench are now included.
      • Algorithms for free energy minimization based prediction of RNA secondary structure
      • Advanced and fully integrated graphical editors for linear and 2D viewing and editing of RNA secondary structures.
      • Advanced prediction of secondary structure using predefined constraints for base pairing.
      • Table showing multiple secondary structures for one sequence
      • Overview of each structure element’s energy contribution
    • Work directly on data on a shared network drive
    • Improvements of annotation editing through the new annotation table.
    • Copy and paste annotations from one sequence to another.
    • New fragment table when doing restriction sites analysis.
    • Secondary peak calling
    • Translation of sequences in a contig improved (reading frames are aligned with consensus sequence, mutations on the amino acid level are shown in red – silent mutations are shown in yellow)
    • New scales for graphs along the sequence (in the Side Panel when viewing protein sequences under “Protein Info”):
      • Surface probability (Emini)
      • Backbone chain flexibility (Karplus and Schulz)
    • It is now possible to create a virtual gel simulating a restriction enzyme digest.
    • PFAM domains now include a link to the PFAM website providing more detail about the domain. The link is available from the Annotation table.
    • Full support for Windows Vista
    • One-click switch between views (e.g. circular and linear sequences views)
    • New annotation table – easy overview and filtering of annotations
    • State-of-the-art layout of annotations
    • Better and more intuitive handling of files (you can now access the files directly on the file system)
    • It is now possible to “Save as”
    • Easily expand selections using the mouse
    • Improvements of restriction site analysis
All the details
  • Data handling
    • It is possible to add new locations to the Navigation Area by clicking the “Add Location” icon in the small tool bar above the Navigation Area. This makes it possible to use any folder directly from within the Workbench. A folder on a shared network drive can also be used enabling sharing of data with other users.
    • If more than one user tries to edit the same file, the second user who tries to save changes will be notified that the file has been changed. This user is then encouraged to use the “Save As” instead.
  • Restriction sites
    • New restriction map object created when doing restriction sites analysis.
      • Restriction maps can be viewed as either fragment tables or virtual gels.
      • Fragments in tables are displayed with graphical illustration of overhangs.
      • When more than one enzyme cut at the same position, fragments are colored red to indicate that the result might differ in an in vitro experiment.
  • Sequence views
    • Possibility to specify own annotation types. The list of annotation types can now be expanded simply by typing the name of a new type.
    • The Edit/Add Annotation dialog has been improved to make it possible to enter more information about an annotation. Following the conventions of the GenBank format, you can now add a number of qualifier/key pairs.
    • You can add links to web sites on annotations. In the qualifier/key part of the annotation dialog, you can simply enter a URL (link) and it will be possible to click on the link in the annotation table and open a browser.
    • More intuitive to edit alignments. Deleting and inserting gaps is now done for the selected sequences only. Deleting part of the sequence now moves the position of the rest of the sequence (instead of introducing gaps)
    • For graphs along the sequence, you can now enter a custom window size. Previously it was restricted to a few options.
    • In sequence views, you can make a selection, right-click and “BLAST Selection” both against NCBI and a local database.
    • Selecting a row in the BLAST table make a corresponding selection in the graphical BLAST view
  • Motif search
    • Regions with N’s are not searched when doing motif searches.
    • Selecting a motif in a motif search table will make a corresponding selection in the sequence view.
  • Primer design
    • It is now possible to set a value for “Maximum pair end annealing” score
    • In alignment-based primer design, it is now possible to specify a “No primers here” region like in the single-sequence primer design. It is available in the right-click menu on a selection.
  • Assembly and sequencing data analysis
    • It is now possible to assemble to a reference sequence with only one read.
    • You can now right-click the name of a sequence in a contig and delete the sequence.
    • Improvements of the contig table: conflicts are now kept in the table after they are resolved. A new field has been added to indicate status as “Resolved”.
    • Single-click editing of single bases is now also possible in normal sequence views (it was previously only possible in contigs).
    • Secondary peak calling. In the Toolbox under “Sequencing Data Analysis”, you find “Call Secondary Peak”. It looks at the peaks in the sequence and is able to detect a “peak within a peak”. This is useful when looking for heterozygous mutations.
  • General use
    • One-click switch between views (e.g. circular and linear sequences views). There is a new row of buttons at the bottom of each view which you can click to switch the view. Pressing Ctrl (Command on Mac) while clicking creates a split view of the two.
    • Pressing Ctrl (Command on Mac) while rolling the scroll wheel of the mouse can now be used to zoom in and out (only possible for mice with scroll wheels).
    • Many right-click menu items have now icons to make it easier to navigate the menus.
    • Simplifying the task of creating a new sequence. Rarely-used elements like “Keywords” and “Comments” have been removed from the dialog, and the two steps have been merged into one.
    • You can now use I (inosine) in nucleotide sequences.
    • Better choices for the resolution of exported graphics.
  • Sequence views
    • Easily expand selections using the mouse. When you have made a selection, place the mouse cursor on the edge of the selection, and you can now adjust the selection. This is also possible for each part of a multiselection.
    • Quick-jump to annotations. In the Side Panel under “Annotation types”, it is now possible to click a quick-jump button which lets you go directly to the annotation. This provides a very quick and easy way of browsing annotations.
    • The names of annotations are now repeated on each new line in a wrapped sequence view.
    • The user can now specify which symbol to use in an alignment consensus sequence in case of ambiguities.
    • In nucleotide sequence views, you can introduce a space for every three characters to visualize codons. In the Side Panel under “Sequence layout” there are now several options for “Spacing”: Every 10 residues, every 3 residues in three reading frames.
    • It is possible to search in text views. In the Side Panel, there now is a “Find” group where you can enter a text to search for.
    • You can now hide labels in sequence views. This is particularly convenient with long sequence names taking up a lot of space.
  • Import and export
    • Pasting simple sequence text (like ATCGTACGTA) in the Navigation Area automatically creates a new sequence.
    • Import and export of view settings (the settings saved in the Side Panel). In the Preferences dialog (available from the Edit menu), in the “View preferences” you can now export and import the View settings.
    • All tables can be exported in a CSV format (semicolon-separated). When exporting sequences in this format, the annotations are exported.
  • Restriction site analysis
    • “Restriction Sites Analysis” has been renamed to “Create Restriction Map” and the dialogs are more intuitive to use.
    • It is now possible to filter the list of enzymes to easily pick a specific enzyme.
    • It is easier to set the number of cut sites for the restriction enzymes to be displayed
    • When you open an enzyme list, you can select a number of enzymes, right-click and “Create New Enzyme List from Selection”. This makes it easy to create subsets of enzyme lists. Combined with the table’s filter, this makes it easy to extract e.g. restriction enzymes from a specific vendor.
  • Data handling
    • Copy an element in the Navigation Area by dragging while pressing the Ctrl button (Command button on Mac)
    • Filter elements in the Navigation Area (to show e.g. only nucleotide sequences). The filter is available from the small tool bar above the Navigation Area.
    • When selecting elements for analysis, only the relevant elements are shown (e.g. only nucleotide sequences are visible when selecting sequences for Restriction Site Analysis).
    • When selecting elements for analyzes (in the select elements dialog), you can right-click a folder and add all the elements in that folder.
    • Possible to sort elements alphabetically
    • One-click renaming of elements. Simply click an element which is already selected, and you can type a new name directly.
    • Recycle bin is now visible and you can easily restore deleted elements simply by dragging to the desired folder.
    • In the File menu, there is a “Save As” menu item. It saves the opened element under a new name.
    • Easily collapse all folders in the Navigation Area by clicking the “Collapse All” icon in the small tool bar above the Navigation Area.
  • Plug-ins and licenses
    • Plug-ins are now installed for all users of a computer.
    • Licenses also apply to all users of the computer.

CLC Combined Workbench 2.2.4

Release date: May 30, 2007
The following has been updated
  • Import of VectorNTI database significantly improved
  • Fixed a problem with SNP BLAST caused by a change at the NCBI server.
  • Fixed error that occurred when trimming away user defined vector sequence.
  • Fixed minor problem in displaying trace files of extremely poor quality.

CLC Combined Workbench 2.2.3

Release date: April 24, 2007
The following has been updated
  • Better support for Windows Vista
  • Improved import of Swiss-Prot files
  • User can now select DNA or Protein sequence for Fasta import
  • Fixed assembly problem when deleting reversed read
  • Minor BLAST changes

CLC Combined Workbench 2.2.2

Release date: March 08, 2007
The following has been updated
  • Improved import of GCG files
  • Improved import of BLAST alias files
  • Workbench starts correctly on AMD64 linux distributions
  • Fixed error when upgrading preference settings
  • Fixed error in motif search if the search string is more than 127 characters
  • Better handling when searching very large BLAST databases
  • Fixed focus problem preventing interaction with Side panel

CLC Combined Workbench 2.2.1

Release date: January 30, 2007
The following has been updated
  • The list of available BLAST database has been updated
  • Now it is possible to use multi-volume blast databases
  • Fixed error when opening a selection of reversed reads in the contig editor.
  • Fixed error when deleting single stranded regions in the cloning editor.
  • Fixed error in the bugsubmission dialog when it was invoked by a workbench crash
  • Fixed error in the preference panel when using empty BLAST url

CLC Combined Workbench 2.2

Release date: December 18, 2006
The following has been updated
  • Possible to install and use plug-ins
  • Possible to develop your own plug-ins using our Software Developer Kit
  • Improved editing of trace data
  • BLAST databases can now be defined by the user
  • Possible to specify the amplicon length in standard PCR
  • BLAST databases can now be defined by the user
  • SignalP and TMHMM is now available through plug-ins
  • Various bugfixes

CLC Combined Workbench 2.1

Release date: November 29, 2006
The following has been updated
  • Automatic annotation of raw sequences with SNPs, DIPs and other types of small scale variations. Annotation is based on user-friendly BLAST against the dbSNP database
  • Better secondary protein structure prediction
  • Additional parameters have been included in melting temperature calculations (Primer design)
  • Improved 3D viewing of molecules; among others including simultanious viewing of sequence structures in 2D and 3D
  • Greatly enhanced web based BLAST. Longer sequences can be BLASTed, the graphical user interface is improved, and the subsequent handling of search results has been improved
  • Automated design of primers and TaqMan probes
  • Enhanced BLAST on local databases. The graphical user interface is improved, and the subsequent handling of search results has been improved significantly
  • You can now save HMM models generated in the Pattern Discovery function (searching for unknown patterns) – this reduces time for future pattern discovery searched significantly
  • Advanced and interactive view of four different kinds of pairwise sequence comparisons:
    • Gaps
    • Differences
    • Identity
    • Jukes Cantor distances

These improvements and changes have been made in CLC Free Workbench and CLC Combined Workbench:

  • Greatly improved data import: Manual work is reduced significantly when importing large amounts of data; e.g, when shifting from old software to CLC-software
  • Much better handling of very large sequences: Much less memory use makes the application smoother to work with
  • Significantly better data handling makes actions like deletion of files and working with many files at a time much faster
  • Inclusion of pre-defined style sheets for the preference panel
  • Greatly improved export of graphics
  • Greatly improved printing
  • Greatly improved file handling (faster etc.)
  • Greatly improved save-function. Among others the option of creating new folders from the save dialog
  • Tables are now searchable
  • All output of analyses can now be shown in table

CLC Combined Workbench 2.0.4

Release date: November 9, 2006
The following has been updated
  • Fixed error with help-files

CLC Combined Workbench 2.0.3

Release date: November 7, 2006
The following has been updated
  • Swiss-Prot parser can now download and handle files from the UniProt (9.0) release (updated file format)
  • Swiss-Prot parser again handles multi-entry Swiss-Prot files
  • Fixed error dialog on exit of the workbench if an external file is deleted while kept open in another program

CLC Combined Workbench 2.0.2

Release date: August 2, 2006
The following has been updated
  • Fixed rare cases where doubleclicking annotations in an alignment resulted in a wrong selection
  • Fixed dialog when stopping BLAST runs in the process area
  • References to BLAST databases are updated due to changes on the NCBI server
  • Corrected check for 3′ end heterogeneity when predicting specific reverse primers based on an alignment

CLC Combined Workbench 2.0.1

Release date: July 18, 2006

These improvements and changes have been implemented in CLC Combined Workbench:

  • BLAST: Expectation values with decimals now works for all locales
  • Nexus parser fully functional
  • Tracefile import updated: Gaps are replaced with wildcards
  • Bootstrap values visible bug fixed
  • Alignment gap-cost overflow management
  • Cut/delete in navigator improved
  • Even more user-friendly import-dialog
  • Atom-count in sequence statistics bug fixed
  • Bug fixed when downloading BLAST hit from graphical BLAST output viewer
  • Attempting to drag more than 100 sequences no longer opens viewers
  • Improved import of nucleotides from Vector NTI
  • Import of oligos from Vector NTI

CLC Combined Workbench 2.0

Release date: July 6, 2006

All improvements below have been implemented in CLC Combined Workbench:

Improvements in CLC Free Workbench and all other Workbenches:
  • All icons have been updated in order to support a more modern and platform-independent look
  • Two or more sequences can now be joined into one
  • Two or more alignments can now be joined into one
  • The history log has been improved, giving an even better overview of past work tasks performed on a given element (an alignment, a sequence etc.)
  • In order to give a better overview of sequences, they are now wrapped to fit the screen as default when they are opened.
  • A large number of tool tips have been added
  • All analyses have now an initial pre-defined setting of parameters. These parameters can be re-applied by the user’s choice
  • Position specific information (e.g. the conservation score on an alignment) on sequences and graphs is now available by pointing to or selecting a position.
  • DNA Strider data and PIR data can now also be exported (earlier only import was available)
  • Import/export of NEXUS data
  • Import of sequences in Staden format
Improvements in CLC Gene Workbench and CLC Protein Workbench:
  • BLAST output can now be viewed in a table format, giving an easy overview of the data
  • BLAST can now be performed on local databases
  • You can now build local BLAST databases
  • Motif searches can now be performed by using regular expressions
  • Motif searches can now be performed by using ProSite patterns
Improvements in CLC Protein Workbench:
  • The 3D viewer has been improved in several ways:
    • Better parsing of PDB data
    • Integration with the 2D sequence viewer
    • Implementation of tooltips on atoms
    • The BLAST of PDB data has been improved
  • The Protein report has been improved significantly and now also includes
    • Signal peptide prediction
    • Secondary structure prediction
    • Transmembrane Helix prediction
    • PFAM search results
Improvements in CLC Gene Workbench:

Primer design

  • Advance analysis of primer properties
  • Alignment based primer design
  • Alignment based TaqMan probe design

Assembly of sequencing data

  • Option of aligning DNA sequencing data to an existing contig. This is especially useful when sequencing multiple exons from the same gene
  • Tabular view of an assembled contig, including variance information. This provides an easy overview of conflicts in the data
  • Improved “Assemble to reference sequence” functionality
  • Option of finding inconsistencies
  • Trimming annotation information is now included

Molecular Cloning and cutting

  • The program now includes a fully integrated 1D DNA Gel Simulator
  • The molecular cloning functionality has been improved

CLC Combined Workbench 1.0.2

Release date: April 19, 2006

All improvements and error fixing described below are implemented in CLC Combined Workbench. These improvements and changes have been made to CLC Free Workbench and all other Workbenches

  • The phylogenetic tree function has been improved: The number of replicates (the bootstrap value) is no longer fixed at 100. Any value can now be chosen.
  • It is now possible to cancel the process when exporting views to graphics file formats such as .jpg, .pdf, and .svg etc.
  • It is now possible to cancel “license upgrade” from within the program (Help menu)
  • When sequences are opened, they are now zoomed to nucleotide level per default. The prior default setting was “fit to width”.

These errors and problems have been fixed in CLC Free Workbench and all other Workbenches

  • Restriction site analysis: In some situations, updating from an older version of CLC Free Workbench to CLC Gene Workbench, CLC Combined Workbench, or CLC Free Workbench 2.5 or 2.5.1, resulted in the program freezing when selecting restriction enzymes. This problem has been fixed.
  • Export of GenBank search parameters did not always work perfectly. This is now fixed.
  • Running different types of CLC Workbenches right after each other could result in errors in some situations. This is now fixed.
  • The user is now told if no hits were found in a database search – e.g. a GenBank search.
  • Help-description in the programs: Users having an older version of JavaHelp installed than JavaHelp 2.0 did sometimes experience missing or in-optimal help-texts. This is now fixed.
  • In a few situations, import of ABI files was not done correctly. This is now fixed.
  • In some situations, resizing of the application changed the toolbar layout. This is now fixed.
  • Naming a workspace with the same name as an existing workspace can now be done without problems.

In CLC Gene Workbench, this has been changed

  • View of trace data: If ”View of protein-translation” is chosen, the amino acids are now located between the sequence and the trace data graphs. This gives a better overview of the translations.

In CLC Protein Workbench, this has been changed

  • The Java 3D program extension is needed in order to view protein-molecules in 3D. Java 3D is however not installed as standard on Mac OS X 10.3.x. A warning is now given if this extension is not present on your computer.