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CLC Main Workbench Changelog

What's new in CLC Main Workbench 7.7.3

Oct 25, 2016
  • Improvements:
  • Updated the restriction enzyme list from REBASE.
  • Bug fixes:
  • Fixed an issue with running BLAST on macOS Sierra.
  • Updated PFAM links reported by the Pfam Domain Search tool.
  • Fixed an issue introduced in CLC Main Workbench 7.7.2 where enzymes listed alphabetically after RdeGBI were missing methylation information.
  • Various minor bugfixes.
  • Advanced Notice:
  • Support for some older operating systems (OS), listed below, will be discontinued in early 2017. Software released at that time and later may still run without issue, but problems experienced due to using an unsupported OS will not be addressed.

New in CLC Main Workbench 7.7.2 (Sep 15, 2016)

  • NEW FEATURES AND IMPROVEMENTS:
  • Workflows:
  • Workflow outputs can now be configured so that subfolders to contain the outputs are created.
  • New placeholders are available when defining the names of workflow outputs: {user}, {host}, and for elements of the timestamp of the output object, {year}, {month}, {day}, {hour}, {minute}, {second}.
  • Placeholders within workflow output names that were previously available only as digits can now be specified using written names: {name} is a synonym for {1} and {input} is a synonyms for {2}.
  • When using the {2} placeholder for custom naming in workflow output elements, only unlocked inputs will be included in the generated name.
  • In the generated pdf showing all the configured parameters of a workflow, entries for parameters connected to a tool or an input element now list the names of the defining elements. Previously the parameter listings for such elements were left blank.
  • Where a tool name has been altered in a workflow, the original name is now included alongside the changed name when exporting workflow parameters.
  • The History view of data elements created using a workflow now includes information about the workflow that created them.
  • The order of the tools in the workflow "Add Element" menu now matches the order in the Workbench Toolbox menu.
  • Improved workflow validation to aid the user in identifying inputs that will be ignored due to the configuration of the workflow elements.
  • Launch:
  • The Quick Launch tool is now found under the Toolbox menu instead of the View menu and a button called Launch that brings up this tool has been added to the toolbar.
  • Analyses can now be launched on data elements listed in the results table of a Local Search by selecting the elements of interest, right clicking with the mouse and navigating through the context menu that appears.
  • Metadata:
  • A "Remove Association(s)" option for removing metadata associations from selected data elements has been added sin the Metadata Elements view in a right click context menu.
  • In the Metadata Find Associated Data view it is now also possible to use Find in Navigation Area when multiple rows are selected.
  • When importing metadata from a spreadsheet with formulas in it, the result of the evaluation of the formula (as displayed in Excel) is now imported rather than the formula itself.
  • General:
  • All NCBI server communication is now encrypted. (NCBI will be moving all web services to the HTTPS protocol on September 30, 2016).
  • The list of enzymes pre-installed in the workbench has been updated from REBASE.
  • The option "is not in list" has been introduced as a new table filtering option.
  • Read group details are now shown on the Element Info view of sequence lists.
  • GenBank import now also allows for file names with 'GBFF' extension.
  • The "Sort folder" tool now uses numerical sorting for filenames prefixed with a number.
  • New placeholders are available when defining the names of exporter outputs: {user}, {host}, and for elements of the timestamp of the output object, {year}, {month}, {day}, {hour, {minute}, {second}.
  • Placeholders within export output names that were previously available only as digits can now be specified using written names: {input} is a synonym for {1}, {extension} is a synonym for {2} and {counter} is a synonym for {3}.
  • BUG FIXES:
  • Fixed an issue that caused characters in sequence names to be rendered incorrectly when a report was exported to Excel.
  • Fixed an issue where the Motif Search tool was incorrectly reporting all match accuracies as either 0% or 100%.
  • The Create New Sequence List button in a broken pair table now works when multiple read groups are involved.
  • Fixed a bug that made graphics export of some plots from reports fail.
  • The Find Binding Sites and Create Fragments tools now properly display mismatches when the primer input is in lower-case.
  • Tables with more than 126 million entries now show a warning that they contain too much data to display instead of leaving the table empty.
  • Fixed an issue where sequences of length zero would cause the Create BLAST Database tool to throw an error. Such sequences are now skipped and will not included in the final database.
  • Fixed an issue in the wizard for the tool Create Entry Clone where a previously used data located on an unmounted location would result in an error message being shown.
  • Fixed a rare issue where some annotations could, but did not necessarily, go missing on sequences with greater than 1000 annotations of a given type on that sequence before the deletion and where the right-click context menu option "Delete selection" was used.
  • Fixed a bug in the "Manage Enzymes" wizard that prevented a user from cancelling the action if "Save as new enzyme list" was enabled.
  • Fixed an issue with the Import Metadata tool where, if a spreadsheet had already been loaded, then selecting the same spreadsheet again did not reload the spreadsheet content.
  • Fixed an issue where it took a long time to open a workbench it it was previouslyclosed when displaying an open table editor that had been sorted.
  • Fixed an issue where right-clicking on a graph in a report and choosing to show "Report", "History" or "Element Info" triggered an error.
  • Fixed an issue with links in tables to the PDB and dbEST databases.
  • Fixed an issue where the save wizard dialog did not pre-select "Save in input folder" when that option was the most recently used one.
  • Fixed an issue where the save wizard dialog did not pre-select "Save in input folder" when that option was the most recently used one.
  • Fixed an issue where, when the Processes tab was hidden and then shown again, any processes listed before the tab was hidden were no longer shown.
  • Fixed an issue that made "Download and save" fail when invoked on a Blast editor.
  • Updated the URL to use for links to UniProt databases.
  • Various minor bugfixes.

New in CLC Main Workbench 7.7.1 (Jun 10, 2016)

  • Bug fixes:
  • Fixed an issue that arose when executing workflows with multiple inputs in batch, where changes to pre-defined, fixed inputs specified during the launch process were not applied.
  • Fixed an issue where the Motif Search tool incorrectly reported all match accuracies as either 0% or 100%.
  • Fixed an issue where sorting a folder while saving into it could trigger an error.
  • Fixed a bug in the batch mode dialog that would lead to an error when problems related to the underlying file or data location were encountered.
  • Advanced notice:
  • From the autumn 2016 release, only 64 bit versions of the CLC Genomics Server, CLC Genomics Workbench, Biomedical Genomics Workbench, CLC Bioinformatics Database and CLC Assembly Cell will be made available. 32 bit versions of these will be discontinued from that time.

New in CLC Main Workbench 7.7 (Mar 31, 2016)

  • NEW FEATURES AND IMPROVEMENTS
  • New tools:
  • Import Metadata - basic and easy metadata import. This tool supplements the tools available in the Metadata Table Editor.
  • IMPROVEMENTS:
  • Metadata related:
  • The use of partial or exact matching schemes can be chosen when associating data with metadata using the Associate Data Automatically option.
  • It is now possible to change the type of a metadata column, even if it already contains values. Conversion is only possible when all existing values in the given column can be converted to the new data type.
  • Usability enhancements in the Metadata Table Editor.
  • Workflow related:
  • Workflow inputs can now be ordered via the Workflow Editor, affecting the order that input information is requested when setting up a Workflow run.
  • Workflows with multiple input elements, where all input elements will be changed per batch, can now launched in batch by right-clicking on the installed workflow name and choosing the option "Run in Batch Mode...".
  • Tools in a Worfklow that have been renamed will have both the new tool name and the original tool name displayed in the Workflow Configuration Editor.
  • General:
  • Performance optimization for sizing phylogenetic trees by metadata
  • The Download Pfam Database tool has been updated to download version 29.
  • Improvements to the way Ensembl IDs are parsed to links in tables: stable Ensembl IDs are now correctly parsed to links for all Ensembl-supported organisms (Ensembl release 83).
  • The options for saving the output from "batch jobs" have been improved. Outputs can now be saved into a specified single folder in addition to the other established save options.
  • All Excel sheets in a document are now imported and each sheet has a table created for its contents.
  • The CSV, HTML and Excel table/tabular exporter now use "Inf" and "NaN" values to replace the ambiguous "?".
  • In the wizard for exporting a table in CSV format, when not exporting all columns, it is now possible to cancel or go back to the previous step while selected columns are loading.
  • Same print settings can now be applied for multiple reports in a single export.
  • The "Manage Resources" tab has been removed from the the Plugin Manager.
  • CHANGES:
  • Workflow related:
  • The Create Scatter Plot tool is now Workflow enabled.
  • The Create MA Plot tool is now Workflow enabled.
  • General:
  • Versions of individual tools are now reported in the history of output objects.
  • Export to clc format now truncates very long filenames.
  • Plots without any data points will now be skipped when rendering reports.
  • RPM package installers for Linux are no longer available.
  • Associate Data Automatically accepts data elements (not folders) as input.
  • The 'Database Fields' label shown in the 'Show Element Info' view has been renamed to ' Local Attribute Fields'.
  • The "Metadata Role Override" parameter that was visible when creating Workflows has been removed.
  • The user can no longer uncheck "export all columns" for input objects that do not support this option. This applies to command line functionality as well, where the user will now receive an error if this is attempted.
  • BUG FIXES:
  • Fixed a bug when the download buttons on BLAST result table view failed for nucleotide sequences.
  • Fixed a frame offset bug that occurred when translating reverse complemented CDS regions into protein sequences.
  • In heat maps it is now possible again to show colors legend to the left and right of the heat map.
  • Fixed a bug that caused the Excel importer to use column names as cell values of the first row.
  • Fixed an issue where open tabs were not correctly ordered after splitting view horizontally or vertically using the View menu or keyboard shortcuts.
  • Fixed an issue where an error was reported if the local realignment tool detected an insertion followed by a deletion in the original mapping. Such positions are now ignored.
  • Fixed an issue where Workflows were not able to remove intermediate data from permission enabled locations unless the top folder was writable.
  • Fixed an issue where the "Show results"option in the Processes tab would lead to an error if the results dataset was very large.
  • Fixed an issue so that double clicking on clc:// urls on Mac OS X now opens the data element in a view in an installed CLC Workbench.
  • Fixed an issue where an error arose when renewing a borrowed network license.
  • Fixed a bug that led to the creation of an empty folder for each excluded batch unit.
  • Fixed a bug that led to the inclusion of the number of excluded batch units in the count of the total number of batch units to be processed.
  • Added missing percentage signs for identities and gaps in Blast text exports.
  • A Workbench Data Location pointing at a file on the system instead of a folder will now appear as unavailable in the Workbench Navigation area instead of throwing an error.
  • Fixed a bug where it was possible to type non-number characters into a number field when starting up a job in the Workbench.
  • An error was previously thrown when encountering blank annotation-values. Blank values are now ignored.
  • Fixed an error that could appear when moving the mouse over annotations in a sequence annotation table.
  • Fixed an issue with Open Copy of Workflow so it now works on all workspaces rather than just the first workspace.
  • Fix an issue that could lead to an error when a job status description changed while a full description was being generated.
  • Fixed an issue with handling dates when importing metadata from Excel format files using the Metadata Table Editor.
  • Fixed a bug that was causing missing report text lines.
  • Fixed an issue where, when the option to "Skip these updates" was checked in the plugin update information window, this information was not saved. This led to the same plugin update information being presented after each Workbench restart if the plugins were not updated.
  • Fixed an error that occurred when pressing the Print button in the Help dialog (Mac OS X only).
  • Fixed an issue where the text area in error dialogs did not expand vertically when the dialog was expanded.
  • Fixed an issue where sub-jobs were not resumed after pausing and resuming a batch process.
  • Fixed an issue where the workflow installer creation keyboard shortcut could be used when it should have been disabled.
  • Fixed a rare issue that could be triggered by switching editor view with a double click.
  • Fixed an issue that caused the 'Use random codon' parameter in the tool "Reverse Translate" to report a null-error.
  • PLUGIN UPDATES AND FIXES:
  • All plugins need to be installed in the new Workbench for compatibility reasons.
  • Changes to freely available plugins:
  • Annotate with GFF: Now supports spaces in annotation names.
  • Batch rename: Fixed an issue where a warning was displayed for entries not modified.

New in CLC Main Workbench 7.6.4 (Oct 17, 2015)

  • Bug fixes:
  • Fixed a bug when the "Search for sequences at NCBI" tool would fail to download nucleotide sequences with the error message "The following sequences were not downloaded correctly: ...".
  • Fixed a problem with the BLAST at NCBI step of the Create Protein Report tool.
  • Fixed an issue leading to an error during VCF export where the data involved had originally been imported from VCF files and the values in the QUAL field were integers.
  • Export of floating-point (decimal) numbers to VCF format were previously dependent on the specified locale. This has been fixed so that the decimal separator now always is a point.
  • When doing automatic association of metadata, the log now shows which metadata rows were not associated with any data.
  • Fixed a bug that prevented metadata manual information to be accessed from within the Workbench.
  • Fixed a bug where doing automatic association using a metadata table stored on a CLC Server would fail.
  • Automatic association of metadata now handles association based on the a prefix of data names rather and exact matching to the whole data name.
  • A metadata table no longer needs a key column for its rows to be manually associated with data elements.
  • An option to override metadata roles previously visible in the configuration of Workflow outputs was removed.
  • Fixed an error happening when a Workbench Data Location was pointing at a file on the system instead of a folder. It will now appear as unavailable in the Workbench Navigation area.
  • Enabled tooltips for all parameters when configuring and executing workflows.
  • The login process from a Workbench to a CLC Server must now complete before opening a clc url will begin.
  • Fix a problem on Macs where the Workbench was not recognized as a custom protocol handler for clc:// urls.
  • Resolved a rare occurring exception that could be triggered by switching editor view with a double click.

New in CLC Main Workbench 7.6.3 (Sep 8, 2015)

  • New features and improvements:
  • Batching on selected elements is now possible: it used to be restricted to selected folders.
  • One can now select "EST" as database when using the Search for Sequences at NCBI tool.
  • The Hierarchical Clustering of Samples tool can now be executed as part of workflows and on the server.
  • Improved memory management when handling large report elements.
  • Tooltips on leaves of phylogenetic trees now display a description of the attached sequence.
  • Numbers are no longer appended to the names of Workflow elements when creating a copy of a Workflow using "Open Copy of Workflow".
  • Metadata Management. Keep track of input files and import meta information for your samples.
  • Bug fixes:
  • Fixed a rare occurring issue where the Workbench would display an error message when installing a 3rd party licensed plugin.
  • Fixed an issue where selecting an entry in a Blast results table could highlight the wrong alignment in the Blast editor if the table had been filtered or sorted.
  • Fixed an issue where clicking on an annotation in the Design Primers editor could give rise to an error message.
  • Fixed an issue where annotations that spanned the ends of a circular sequence would be incorrectly placed in the Circular Sequence View.
  • Fixed a bug that caused the workbench to freeze if certain sequences were displayed in circular view with radial rendering of labels.
  • Fixed exported reports having the wrong author in certain situations.
  • Fixed an issue whereby Create Box Plot and Principal Component Analysis could sometimes be run with illegal arguments, leading to an error message.
  • The output of the Reverse Complement Sequence tool now gets the suffix -RC attached to the name of the input instead of -1 before.
  • Fixed a bug in the Predict Secondary Structure tool when the option to calculate the partition function was selected for long molecules (>1000 nucleotides).
  • Fixed an issue where one could not zoom in after zooming out fully on very large workflows.
  • Fixed an issue that prevented a root folder on Windows drives from being used as a File Location.
  • Fixed an issue where updating an existing installation on Windows would result in the .vmoptions file being deleted, which makes the Workbench run with the default Java configuration.

New in CLC Main Workbench 7.6.2 (Sep 8, 2015)

  • Bug fixes:
  • Added a work around to a java issue that occasionally resulted in the Workbench displaying an uninformative error and requiring a restart to continue working.
  • Fixed an issue with running BLAST at NCBI where an NCBI-generated error about their CPU usage limit being exceeded was not being reported transparently and a result of "no hits" was being reported instead.
  • A fix was applied to avoid an exception in circumstances when the cleanup of downloaded files from BLAST failed.
  • The Reverse Translate tool ignored any genetic code specified in the codon frequency tables. All reverse translation would thus default to the standard genetic code.
  • When installing a workflow with bundled data, it is no longer possible to select a read-only folder for storing the data.
  • Fixed wrong display of "Supported format" when exporting elements from either the Folder Editor or the Local Search Editor.
  • Fix of potential wrong file being saved when editing a file found via the Local Search Editor.
  • Plots inside reports are now shown with their saved side panel settings.
  • Fixed saving different line colors in plots through the side panel.
  • Side panel option to show legends for a plot with more than 10 samples is now enabled.
  • Fixed an issue that led to an error when rendering plots for empty data sets.
  • Fixed an issue where the "Empty Recycle Bin” option was sometimes incorrectly unavailable.

New in CLC Main Workbench 7.6.1 (Apr 16, 2015)

  • New features and improvements:
  • The GTF exporter is now available for the Main Workbench.
  • Transcriptomics experiment and sample tables can now be sorted, even with large numbers of rows.
  • Improved Excel, HTML and tab delimited export of variants (Choose only the annotations/columns you need).
  • Bug fixes:
  • Fixed an error affecting the "Cut Sequence Before/After Selection" tool in the Cloning editor.
  • Fixed bug where a left-click quickly followed by right-click was interpreted as double-click on OS X (in the persistence search result list, in the toolbox tree, and in the workflow editor).

New in CLC Main Workbench 7.6 (Feb 24, 2015)

  • New features and improvements:
  • Tracks:
  • Consistent output when enriching variant tracks and annotation tracks with extra table columns. Output tracks from these tools now have the same number of added table columns and the columns will always be in the same order. Previously, if an added column had empty values for all variant rows, it would have been removed from the final table, resulting in varying number and relative order of additional columns when multiple samples were processed with the same tools/workflows. All columns are retained now, facilitating downstream processing of exported tables, and providing immediate visual reference as to which enrichment/annotation tools have been applied, even if they did not produce any results for a particular sample.
  • Tables for variant tracks and annotation tracks can now sort and filter columns with cells containing multiple numbers.
  • Improved the track viewer for variant tracks to show the sequence alteration on the rendered variant.
  • Graph tracks now show negative values filled upwards to y=0 (as expected).
  • Increased decimals for numbers when exporting table to CSV, tab delimited text, and Excel.
  • Improved reporting of errors related to low disk space.
  • Workflows:
  • When installing a workflow in the workflow manager, the newly installed workflow is automatically selected.
  • The "Run" button in the workflow editor does not require a saved workflow anymore to be enabled.
  • In the execution wizard of a workflow the "Reset to default" button is now active.
  • All icons in the workflow editor are now on the left side.
  • Introduction of snippets: Parts of workflows can now be saved as a snippet and reused in other workflows.
  • Installed workflows: It is now possible to create a copy of an installed workflow and open the copy in the view area by clicking once and then right-clicking on the installed workflow in the toolbox. This brings up the option "Open Copy of Workflow".
  • New features for the 3D molecule viewer:  
  • Align to Existing Sequence makes it possible to connect a 3D protein chain to a sequence, sequence list, or an existing alignment.
  • Transfer Annotations makes it possible to create atom groups from sequence annotations (and vice versa) for connected sequences.
  • Improved layout of the property viewer.
  • Improved PDB import of water molecules, DNA/RNA, and saccharides.
  • When importing PDB files, the resulting Molecule Project now contains citation information (PDB ID and primary reference), which can be found in the 'Show History' view.
  • MA plots, scatter plots and histograms can now accept expression tracks as input.
  • Batching: Processes tab and analysis execution logs now display batch names in addition to analysis names for enhanced clarity.
  • The External Application Client Plugin is now available directly from the Workbench Plugin Manager.
  • Bug fixes:
  • Fixed display problem in read mappings showing too many hidden insertions (as vertical black lines) in certain overlapping paired reads.
  • Fixed problem with links and text in tables that were being cut off when succeeding a link.
  • Restriction site analysis: The values "Cut position(s)" column of the restriction site analysis table now behaves like numbers instead of text, meaning sorting and filtering works.
  • Workflows:
  • In the workflow editor the "Reset to default" now always reverts to the right names.
  • In the workflow editor the validation is now correctly triggered when changing the configuration of an input element.
  • The workflow editor can now open workflows in which the graphical view of the workflow is corrupt.
  • Fixed an exception which could occur during workflow migration.
  • Data with the same name can now be bundled multiple times in a workflow installer.
  • Previously when a plugin contained custom actions and a workflow, the workflow could not be installed. This has been fixed.
  • Fixed problem with unlocked output names that previously could not be configured during execution of a workflow.
  • A workflow with configured data from a server is now automatically validated when connected to the server (when opened in the editor). Previously the workflow had to be closed and reopened first.
  • The original workflow file included in a workflow installer can now be exported directly without having to restart the workbench in advance.”
  • A problem with saved table settings that sometimes did not work has been fixed. The bug fix includes a more robust/generic way of saving table settings with different columns. To fix this problem, existing saved table settings should first be loaded on an object where it works (i.e. has the same columns as when it was saved); and then the table settings should be saved with the old name to overwrite the settings.

  •  Fixed an error that could cause batch processing to open all results rather than saving them. 
Fixed problem going back in the wizard for the "Find Binding Site and Create Fragments" tool.
  • Fixed error occurring when removing an unsaved reads track from a track list.
  • Metadata for phylogenetic trees: A bug has been fixed with import of metadata containing column names with colons.
  • Fixed error when showing protein translations of annotations shorter than 3 bases.
  • Search for PDB Structures at NCBI has been fixed to correctly show PDB deposit date and organism type. 

  •  Fixed a bug that in some cases caused an error when annotating read sequence lists with the GFF/GTF/GVF annotation tool. 
  • Hypergeometric test on annotations: Fixed a rare error that occurred for some datasets containing annotations of the form: '1234 // abc'.
  • The alignment editor view and alignment primer design view now have independent settings.  

  • Plugin updates and bug fixes:
  • TRANSFAC Plugin updated and now has two modes of operation: "Classic" and "Genomic". Classic mode is the legacy mode taking sequences as input and annotating these sequences. The new Genomic mode takes regions on a genome (an annotations track) as input. In addition, in both modes it is now possible to specify global thresholds of similarity score which can be used to filter the annotations included in the output.
  • A bug has been fixed with import of metadata containing column names with colons in the Metadata Import plugin.

New in CLC Main Workbench 7.5.1 (Oct 28, 2014)

  • New features and improvements:
  • It is now possible to run a workflow without an optional input.
  • Bug fixes:
  • The AAC tool did not annotate variants in 3' UTR with their DNA-level change using the HGVS c.xxx format. This affects any analysis done with Gx 7.5 or earlier based on ENSEMBL CDS tracks from older versons. The AAC analysis should be redone using Gx 7.5.1 for correct annotation.
  • Pfam filtering bug fixed. Previously, Pfam only reported the first domain of each type in a query and as a consequence many domains were missed. We recommend that users whose research depends on Pfam annotations re-run the tool on their data.
  • Fixed a bug in the 'Maximum Likelihood Phylogeny' tool that failed when generating bootstrap values for certain input alignments.
  • Fixed problem with scrolling to the relevant files when selecting objects as parameters in tool wizards.
  • The Blast text results have been improved so they show the correct query and subject positions regardless of strand.
  • Fixed a problem that prevented BLAST operations when choosing to run these on the CLC Server.
  • It is now possible to run a workflow without an optional input.

New in CLC Main Workbench 7.5 (Aug 28, 2014)

  • New features and improvements:
  • Workflows:
  • The input information is now shown in the preview dialog and also exported to all formats.
  • It is now possible to edit the workflow input name by right-clicking on the input name in the workflow.
  • Workflows as such can have multiple inputs (though this will disable the batch functionality).
  • Data can now be directly bundled with a workflow installation. This means that reference data can be packed and shared together with a workflow (only recommended for small data).
  • A workflow input can be pre-configured. If kept unlocked, it can be used to give a default when executing the workflow.
  • A text field has been added to the side panel, where you can search for elements in the workflow. A found element will be centered and highlighted.
  • A new editor was added to the workflow to make it easier to check the configuration. The new editor can be accessed from the lower left corner of the View Area and lists all configuration parameters.
  • Workflows can be packaged with a plugin and will get installed with the plugin simultaneously.
  • Workflows installed on the server now have an overlay icon in the workbench, to make them easily distinguishable from workflows installed in the workbench.
  • The execution of a workflow in the workbench and on the server have been unified to have the same behavior regarding logs, intermediate results and output naming.
  • Locked settings in the workflow wizard are now again hidden per default when executing the workflow, to give a cleaner, simpler look to the configuration. When expanding, all parameters are displayed.

  • Protein Analysis, Pfam domain search:
  • Pfam Domain Search now uses HMMER3 and the latest Pfam database that can be downloaded with the new tool "Download Pfam Database".
  • Searching multiple sequences is significantly faster.
  • New filters are available in the improved Pfam Domain Search tool to enable generation of the same results as the online tool.
  • Local Search enabled from the menu bar now includes filtering on "Path".
  • Advanced filtering on tables now includes the option to filter for a space, comma or semi-colon delimited lists of terms.
  • Zoom tools redesign: The “Zoom to selection” feature is now also available for sequences, sequence lists, alignments and read mappings.
  • The tracks info panel, with track names in the left side of the track, now wraps information instead of showing a scroll bar.
  • Saving/applying side-panel settings for tables now works for different tables that share some columns. 
  • Copy operations can now be stopped.
  • Output from "Reverse Translate" can now be a Sequence List.
  • Import of Example Data and imports done through dragging files into the workbench and dropping them in the Navigation Area will no longer block the user interface while executing. Instead, the import happens as a background process that can be monitored and controlled via the Processes tab in the lower left corner.
  • CLC workbenches now support high resolution displays such as Apple retina displays of all data shown in the View Area (including tooltips).
  • Improved error message in the Empirical Analysis of DGE tool in case of invalid expression values in experiments (occurs rarely).
  • More informative naming of coding region translations produced by the tool Translate to Protein. The name for a coding region translation consists of the name of the input sequence followed by the annotation type and finally the annotation name.
  • Genetic codes: The list of NCBI translation tables has been expanded to include  translation table 25 "Candidate Division SR1 and Gracilibacteria" (See: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c).
  • Improved error messages due to low disk space.
  • Bug fixes:
  • The right-click menu on certain annotations in tracks was not working when viewing a single track. This has been fixed.
  • Icons in the workflow editor are now scaled consistently when zooming in or out.
  • Several issues with the validation display in the workflow editor have been fixed.
  • A bug has been fixed in the workflow configuration wizard. Previously the input was not taken into account when deciding which parameters were enabled.
  • Fixed problem where the "space" key did not trigger "Find Conflict" in the stand-alone read mapping editor.
  • Fixed stand-alone read mappings not showing mismatches and insertions in the overflow graph.
  • 'Replace input sequences with result' in Cloning Editor no longer fails.
  • Multi-sequence BLAST search results (BLAST tables) are now exportable as plain text.
 
  • Changes:
  • Due to upgrade to Java 7,  Windows Server 2003 and OSX 10.5.8, 10.6 are no longer supported by Oracle. Hence, the system requirements are now: Linux, Windows Vista, Windows 7, Windows 8 or Windows Server 2008, or Mac OS X 10.7 or later.

New in CLC Main Workbench 7.0.3 (May 14, 2014)

  • Bug fixes:
  • Fixed error that caused selections in views not to be centered in the middle of the view.
  • Fixed bug that caused a crash in the Reassemble Contigs tool
  • Fixed bug that made the Workbench crash when viewing tables under certain circumstances
  • Fixed problem with "Find" on stand-alone read mappings with a circular reference and sequence lists containing circular sequences.

New in CLC Main Workbench 7.0.2 (Mar 19, 2014)

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

New in CLC Main Workbench 7.0.1 (Mar 17, 2014)

  • Fasta export:
  • Fasta export with trimming is now much faster and consumes less memory
  • Fasta export now reports progress while executing
  • When the "Remove trimmed regions" option is set, the Fasta export will ignore sequences in which all nucleotides are covered by a Trim annotation
  • Translate to Protein (Batch Process):
  • The wizard now has options for specifying whether to translate the coding regions or extract translations from the annotations
  • The log has been made more detailed and informative
  • If the result is just a single protein sequence, the output will be just that, otherwise all sequences are output as a list
  • If the tool estimates that the number of protein sequences to be produced is greater than 1.000.000, it will create protein sequences without history, and it will not copy the common name, latin name, and taxonomy fields
  • The PDB importer has improved support for custom residues
  • Bug fixes:
  • Fixed missing icon for "Metadata Import" in the phylogenetic tree table
  • Multi BLAST results table: the missing "Description (E-value)" field is displayed again in the table output
  • Fixed a bug that made PDB import fail on workstations with Turkish Locale settings

New in CLC Main Workbench 6.9.2 (Jan 23, 2014)

  • Bug fixes:
  • Fixed: Error message when running analysis on experiments (statistical tests, clustering etc.)
  • The folder used by the Workbench for storing log and settings files on Windows 8 has been updated to follow conventions for Windows 8 which is identical to Windows 7. Any existing settings will be copied to the new location automatically.
  • Fixed various problems related to launching the Workbench through Java Webstart.
  • Fixed: Opening a search view for searching sequences at NCBI would sometimes fail.
  • Fixed various stability and performance problems of Maximum likelihood phylogeny.
  • Fixed problem that caused a crash with extract consensus sequence tool with certain parameter configurations and with read mappings with no reads.
  • Fixed a bug in the Assemble Sequences tool causing some data sets to produce inferior contigs.

New in CLC Main Workbench 6.9.1 (Oct 23, 2013)

  • New features:
  • Heat maps: It is now possible to show a legend on a heat map.
  • Changes:
  • When importing Genbank nucleotide sequences, the Workbench will determine whether it is DNA or RNA based on the sequence rather than the description in the file.
  • Bug fixes:
  • Fixed: Trimming sequencing data for vector contamination from UniVec failed
  • Fixed: GFF export failed.
  • Fixed: Copying information from the Folder Contents view did not work.
  • Fixed: out of memory error when performing bootstrapping with ML tree construction methods.

New in CLC Main Workbench 6.9 (Sep 2, 2013)

  • New features:
  • Workflows:
  • Automatic adjustment of layout in workflows. It is now (again) possible to adjust the connected workflow elements automatically. Right click in the workflow editor to access a menu with the option "Layout". Clicking on "Layout" will adjust the layout of the workflow. The layout can also be adjusted with the quick command Shift + Alt + L.
  • Automatic update of tools in workflows. Tools in existing workflows will automatically be updated when opened from the Navigation Area. If new parameters have been added to the updated version of the tool, these will be used with their default settings. A workflow can be kept in its original form by saving the updated workflow with a new name as this will ensure that the old workflow is kept rather than being overwritten.
  • Information: In the “Manage Workflows” dialog a new tab has been added providing information about the workflow (such as when it was built and which version of the workbench was used).
  • Highlight used elements: In the Side Panel under “View mode” it is now possible to select “Highlight used elements”, which will show all elements that are used in the workflow. Unused elements are grayed out. The “Highlight used elements” can also be activated with the quick command Alt+ Shift + U.
  • Highlight Subsequent Path: Is a further development of the old option “Mark Subsequent Path”.  If you right click on the name of one of the tools in a workflow, it is possible to select “Highlight Subsequent Path”, which will highlight the path in the workflow from the tool that was clicked on and further downstream.  All other elements in the workflow will be grayed out.
  • Create Installer: A workflow can now be installed directly from the workbench. This can be done with the “Create Installer” button (or the quick command Alt + Shift + I). Three options exist in the “Create Installer” dialog: 1) Install the workflow on your local computer, 2) Install the workflow on the current server (requires that you are logged on to the server and that you are the administrator), and 3) Create an installer file to install it on another computer.
  • Export can now be part of workflows.
  • Workflow enabled elements can be dragged directly from the Toolbox into the workflow editor.
  • Workflow images can be copied from the editor by using Ctrl + C (copy) and pasted into the desired destination with the Ctrl + V command.
  • All elements can be removed from the workflow with the shortcut Alt + Shift +R.
  • Reinstallation of modified workflows can now be done directly with the “Create Installer” function. A pop-up dialog provides the option to make "forced import" of an already installed workflow.
  • Speed improvements in the workflow editor means that the user experience when editing large workflows has been greatly improved.
  • New tools that are now workflow-enabled:
  • Classical Sequence Analysis, Alignments and Trees
  • Create Tree
  • Maximum Likelihood Phylogeny
  • Classical Sequence Analysis, General Sequence Analysis
  • Extract Annotations
  • Classical Sequence Analysis, Nucleotide Analysis
  • Reverse Complement Sequence
  • Reverse Sequence
  • Molecular Biology tools, Sequencing Data Analysis
  • Assemble Sequences
  • Assemble Sequences to Reference
  • Secondary Peak Calling
  • Transcriptomics Analysis, General Plots
  • Create Histogram
  • 3D Molecule Viewing: The integrated viewer of structure files, the 3D Molecule Viewer, has been completely redesigned. The Molecule Viewer offers a range of tools for inspection and visualization of proteins and other molecules stored in structure files from the Protein Data Bank (PDB).

  • The "Assemble Sequences" and "Assemble Sequences to Reference" tools are now batch, server and workflow enabled.
  • Assemble Sequences: Trimming is no longer integrated with the “Assemble Sequences” tool. This means that trimming must be done separately with the “Trim Sequences” tool.
  • Export framework redesigned:
  • Export of multiple files: you can export several files in one go. The naming of the file will default to the name used in the Navigation Area of the Workbench, but the user can specify a naming pattern to use instead.
  • Export formats: A new column “Exports selected” has been added to the “Select exporter” table that indicates with a “Yes”, “No” or “Partly” whether the currently selected element can be exported with the given exporters. Partly means that you have made a selection of elements where only some of them can be exported by the selected exporter.
  • Improved usability with a quick-select dialog for choosing the right export format. The dialog includes a  description of each exporter that can be quickly filtered.
  • Export can be integrated into workflows
  • Support for direct compression of exported files in zip and gzip.

  • The folder viewhas been improved with the following:
  • It is now possible to drag and drop objects from the folder editor. This will create a copy of the objects at the selected destination.
  • Attribute columns will be left empty if the attribute has not been defined (previously attribute values that had not been defined were set to 0 and checkboxes were shown as unchecked).
  • A new column showing the first 50 residues of each sequence has been added as an option.
  • The column with the name “Length” has been renamed to “Size”.
  • The column “Size” shows the length of a sequence, or for sequence lists, the number of sequences e.g.:
  • Sequence or contig lists: the number of sequences/contigs
  • Read mappings: the length of the consensus sequence
  • Alignments: the length of the alignment
  • The Side Panel “Save/Restore Settings” functionhas been expanded with a new feature:
  • The “Save/Restore Settings” function (found at the top of the Side Panel) has been redesigned. It is now possible to save settings in two different ways. 1) The settings can be saved for this element type in general, e.g. for a track it would be save settings “For Track View in General”. In this way the settings will be applied each time you open an element of the same type, which in this case means each time one of the saved tracks are opened from the Navigation Area, these settings will be applied. These “general” settings are user specific and will not be saved with or exported with the element. 2) Settings can be saved with the specific element only e.g. for a track it would be save settings “On This Track Only”. The settings are saved with only this element (and will be exported with the element if you later select to export the element to another destination).
  • Alignments: If you have one particular sequence that you would like to use as a reference sequence, it can be useful to move this to the top. This can now be done automatically by right clicking on the sequence name and then selecting “Move Sequence to Top”.
  • The Sequence List Table has been improved with a new feature. A new column showing the first 50 residues of each sequence has been added as an option.
  • Phylogenetic trees:
  • Create Tree now support the Kimura 2-parameter substitution model for DNA sequences and Kimura's distance estimate for protein sequences (Kimura 1983).
  • Construction Maximum Likelihood phylogenies from protein sequences.
  • The following Plug-ins are now fully integrated in the Workbench:
  • Extract Annotations

  • Improvements:
  • Scrolling in read mappings: The mouse scroll speed through read mappings can now be performed with increased speed. Shift + Alt + Mouse wheel scroll makes the scroll 10x as fast as when using Alt + Mouse wheel scroll. When zoomed all the way in, each mouse wheel step scrolls 10 rows.
  • Sort Sequences by Name: The multiplexing tool now allows a delimiter between group names in the “Sort Sequences by Name” wizard. This means that the selected group names are separated by an underscore. Previously all selected group names were merged without any delimiter.
  • Cloning: The cloning editor can now work without having a designated vector. In essence this means that when no vector is selected you go directly in “Stitch mode” when a fragment has been selected, whereas you go in “Cloning mode” when a cloning vector and a fragment are selected.
  • Renaming of data in the Navigation Area by clicking twice has been improved. Previously, you could accidentally enter rename mode when the intention was to get focus in the Navigation Area. Now, you can only trigger rename by clicking when the Navigator has focus.
  • Extract consensus sequence tool:
  • It is now possible to use the quality scores when resolving conflicts or disagreements between reads with “Insert ambiguity codes”. Previously, “Use quality scores” could only be selected when using the “Vote” option for conflict resolution.
  • Low coverage regions are now annotated in the consensus sequence produced.
  • The Extract Consensus Sequence dialog is now shown when extracting the consensus sequence when right-clicking a selection on the reference sequence in the mapping view, enabling the user to extract part of the consensus sequence.
  • The Extract Consensus Sequence dialog is now shown when extracting the consensus sequence when right-clicking the name of the consensus or reference sequence, or when clicking the Extract Consensus button in the mapping table. The right-click menu option on the consensus to Open Sequence Including Gaps has been removed, since this functionality is now covered by the Extract Consensus Sequence tool.
  • When using the “Translate to protein” tool, the max limit has been raised to 1GB.
  • The sequence action "Open Copy" has been removed and "Open This Sequence" has been renamed to "Open Sequence".
  • The alignment tool is now more memory efficient.
  • Tables: Improved auto-adjustment of the column width (based on content and number of columns).
  • Read mapping: The status bar in the lower right corner now shows the corresponding positions on the reference/contig sequence.
  • BLAST has been upgraded to BLAST+ 2.2.28 that includes a number of improvements and bug fixes. A full list of BLAST+ 2.2.28 changes can be viewed at http://www.ncbi.nlm.nih.gov/books/NBK131777.
  • Usability improvement of simple table filtering:
  • A dedicated filter button has been added to apply the filter directly without having to wait until the filter is automatically applied
  • For tables with more than 10000 rows, the filter will not be applied automatically after a delay. Instead, there is a helping text asking the user to apply the filter through the "Filter" button. This avoids premature filtering before entry of the filter text has completed. Since filter can take some seconds for large tables, this used to be an annoyance because the user would have to wait until filtering was done to complete the entry.
  • Phylogenetic trees:
  • Bootstrapping with the "Maximum Likelihood Phylogeny" is now possible.
  • Bootstrap values are now displayed in percent instead of absolute numbers.
  • Bug fixes:
  • Numbering of amino acids when calculating amino acid changes was wrong for coding regions spanning the starting point of circular chromosomes. We recommend running amino acid calculation again. Please note that the actual amino acid change is called correctly, only the numbering is affected.
  • PDF export of the history of a result did not include the name and version number of the Workbench that produced the result.
  • Phylogenetic trees:
  • The Juke-Cantor distance estimate now ignore all positions containing gaps in pairwise alignments.
  • Disabled substitution rate estimation when the corresponding option is deselected by the user in the Maximum Likelihood Phylogeny tool.
  • Fixed a bug that caused branch lengths to be estimated incorrectly for ML trees.
  • Changes:
  • System requirements for Linux has changed. From this release, SuSE is supported from version 10.2. This was previously version 10.0.
  • Secondary Peak Calling: The parameter “Fraction of max peak height for calling”, in the “Secondary Peak Calling” wizard,  has been changed to use the interval 0-1with 0.2 as default setting. Previously the interval was 0 – 100 with 20 as default setting.

New in CLC Main Workbench 6.8.4 (May 23, 2013)

  • Fixed problem in workflows: it was not possible to configure all elements when running a workflow that branched after the input element.

New in CLC Main Workbench 6.8.3 (May 9, 2013)

  • Bug fixes:
  • Description text in progress area is now making full use of available width of the progress area
  • Handling of line breaks in annotation notes improved
  • On Linux: User interface text has been changed to not use bold font to make a better visual appearance
  • Annotation tracks and variant tracks created in CLC Genomics Workbench can be displayed in a table

New in CLC Main Workbench 6.8.2 (Apr 3, 2013)

  • Improvements:
  • Fragments generated from restriction site analysis can now be opened in batch. When multiple rows in the fragment table are selected, the right-click menu option will now create a sequence list with all the selected fragments.
  • For alignments, mappings, BLAST results 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 fixed:
  • Several errors related to workflow configuration and execution have been fixed.
  • Errors related to managing Workspaces have been fixed.
  • Annotations were added by the Find Open Reading Frames tool, even though the option to add annotations was not selected. This is now fixed.
  • Fixed an out-of-memory problem in the Create Alignment tool.

New in CLC Main Workbench 6.8.1 (Jan 23, 2013)

  • Improvements:
  • 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.

New in CLC Main Workbench 6.8 (Jan 11, 2013)

  • New features:
  • Workflow: there are several important new features for workflows
  • It is possible to control which parameters should be locked or unlocked. This means that the creator of the workflow can decide which parameters should be left open for adjustment when the workflow is executed.
  • Usability of workflow editor greatly improved
  • There is a grid for helping layout
  • Visual indication of the number of possible connections as input to a workflow element
  • Visual indication to show if parameters have been changed
  • Handles for dragging and connecting elements have been made more clear
  • Side Panel for controlling grid layout and switching on compact visualization of workflow elements
  • You can high-light selected paths in a workflow
  • It is now an option to attach the workflow design file with the installer to allow users edit the workflow
  • There is a special icon for workflows in the Toolbar to make the creation and installation of workflows more visible
  • Several tools are now workflow-enabled:
  • Find Open Reading Frames
  • Translate to Protein
  • Convert to RNA
  • Convert to DNA
  • 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.
  • Alignments can be used as input for finding primer binding sites.
  • Export now has progress and can be canceled. 
  • BLAST results and 3D structures can be exported as text.
  • Batching: Previously, results where saved in the same folder as the input data. This can now be changed and a new save folder can be specified. Sub-folders will be created for each batch unit.
  • The limit for the cloning editor has been increased to 6,000,000 bases (from 4,000,000 bases).
  • Create Expression Clone (LR) from Gateway Cloning produces sequence object rather than a list
  • Shortcut key for Translate to Protein has changed from Ctrl + Shift + T into Ctrl + Shift + P.
  • Bug fixes:
  • Fix to the proxy settings recognition meaning that Download of BLAST databases now work 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.

New in CLC Main Workbench 6.7.2 (Jan 3, 2013)

  • 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.

New in CLC Main Workbench 6.7.1 (Sep 7, 2012)

  • 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

New in CLC Main Workbench 6.7 (Aug 10, 2012)

  • New features:
  • Workflow
  • 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 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.
  • Improvements:
  • 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
  • Pearson coefficient displayed in scatter plots
  • A new translation table added: Pterobranchia mitochondrial (see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG24)
  • CLC URL handling in Workbench: In the installer, you can choose to use the Workbench to open files from CLC URLs (clc://). This can be used when working on a CLC Genomics Server, for example, to provide a link to a dataset that can then be opened through the Workbench.
  • Bug fixes:
  • Various bug fixes.

New in CLC Main Workbench 6.6.2 (Apr 11, 2012)

  • Improvements:
  • 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.
  • Keyboard shortcuts for Reverse Complement (Ctrl + R) and Translate to Protein (Ctrl + Shift + T) tools. See the full list of keyboard shortcuts.
  • 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.

New in CLC Main Workbench 6.6.1 (Feb 24, 2012)

  • Minor improvements:
  • 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: Trimming tool in Sequencing Data Analysis does not add annotation to sequences when the full sequence should be discarded.
  • Fixed: Opening external files (e.g. pdf files or Word documents) with spaces in the file name does not work on Windows.

New in CLC Main Workbench 6.6 (Feb 14, 2012)

  • 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
  • New and improved 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 in CLC Main Workbench 6.5 (Nov 29, 2011)

  • 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"
  • 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.

New in CLC Main Workbench 6.2 (Oct 12, 2011)

  • 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 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.

New in CLC Main Workbench 6.1.1 (Sep 23, 2011)

  • 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.

New in CLC Main Workbench 6.1 (Jun 22, 2011)

  • 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
  • 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

New in CLC Main Workbench 6.0.2 (Apr 5, 2011)

  • 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

New in CLC Main Workbench 6.0 (Jan 26, 2011)

  • Cloning tool re-designed to make it easier and faster to perform restriction cloning Read more
  • Restriction sites used to select target vector and fragment. Read more.
  • Sequences can now be displayed in circular mode in the cloning editor. Read more.
  • Only one sequence displayed at a time (there is a list at the top of the view to switch between sequences). Read more.
  • Option to clone several fragments and adjust overhangs and orientation in one dialog. Read more.
  • New cloning tutorial available for a quick introduction. Read more.
  • BLAST tools have been redesigned
  • New Blast Database manager for easy administration and management of local BLAST databases. Read more.
  • More user-friendly way of creating and accessing local BLAST databases. Read more.
  • 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 here.
  • 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.
  • Motif search available in Side Panel
  • Dynamic annotations will be added for motifs defined in the Side Panel (similar to restriction sites). Read more.
  • Use motif lists to add your own motifs to the Side Panel.
  • Annotation table now available for sequence lists, contigs, BLAST results and alignments. Read more.
  • Batching functionality available for selected tools. Read more.
  • 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. Read more.
  • 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). Read more.
  • The default database of restriction enzymes can be expanded (requires manual edit of database file). Read more.
  • The default set of codon frequencies can be expanded (requires manual edit of table files). 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

New in CLC Main Workbench 5.7.1 (Oct 8, 2010)

  • Improvements:
  • 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.
  • Bug-fixes:
  • 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

New in CLC Main Workbench 5.7 (Jun 17, 2010)

  • 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
  • Bug-fixes:
  • 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

New in CLC Main Workbench 5.6.1 (Feb 5, 2010)

  • 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.

New in CLC Main Workbench 5.6.0 (Dec 15, 2009)

  • 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
  • Bug-fixes:
  • 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).

New in CLC Main Workbench 5.5.0 (Oct 8, 2009)

  • 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.

New in CLC Main Workbench 5.2.0 (Aug 18, 2009)

  • 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:
  • You can now perform different clusterings on an experiment and save them all. In the Side Panel you can switch between the different clusterings to show the corresponding heat map.
  • Terminology change in the clustering dialogs: "similarity measure" and "cluster distance metric" are replaced by "distance measure" and "cluster linkage", respectively.
  • Annotating samples or experiments for expression analysis:
  • This is now possible even if the number of features doesn't match the number of annotations
  • You can now decide which column in the annotation file to use for matching to the sample or experiment. Because of this extra option, you can no longer include an annotation file when setting up an experiment. You need to add the annotations afterwards
  • 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

New in CLC Main Workbench 5.1 (Jun 2, 2009)

  • Data formats: Data generated with version 5.1 cannot be read in earlier versions
  • New features:
  • Implementations of statistical tests for comparing expression levels of count-based expression measures as may be produced in RNA-seq
  • Kal's test for differences of proportions in single sample to single sample comparisons.
  • Baggerley's test for differences of proportions in two groups with replicates comparisons.
  • "Reverse Contig" has been renamed to "Reverse Complement Contig." Functionality is un-changed.
  • Exporting coverage graph to csv file now has an option to include or exclude gaps. Excluding gaps will make the file use the reference sequence coordinates
  • Import of Illumina expression bead arrays and bead array annotation files
  • Import of Affymetrix Chp files (CHP / PSI)
  • Transformation of expression values now supports square root transformation.
  • Better feedback on processes: there is a tool tip showing details and start time.
  • Translation of DNA to protein in sequence views can now be set to follow existing CDS/ORF annotations.
  • Much improved memory performance and processing time of large data sets
  • Improved performance when handling trace data. Trace now take up 50 % less disk space. This means that the data is opened and saved much faster and less memory is used.
  • 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).
  • UniProt search works again.

New in CLC Main Workbench 5.0.2 (Mar 12, 2009)

  • Updates:
  • 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.

New in CLC Main Workbench 5.0.1 (Feb 27, 2009)

  • 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.

New in CLC Main Workbench 5.0 (Jan 28, 2009)

  • 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.
  • Assembly:
  • 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.
  • Plug-ins:
  • 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.

New in CLC Main Workbench 4.1.2 (Nov 20, 2008)

  • 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.

New in CLC Main Workbench 4.1.1 (Oct 2, 2008)

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

New in CLC Main Workbench 4.1 (Sep 18, 2008)

  • Improved performance when handling large data sets.
  • Contigs can be exported in ACE format.
  • Export of graph data points in csv format.
  • 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".
  • 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.
  • Fixed bugs related to contig editing.
  • Various bug-fixes.

New in CLC Main Workbench 4.0.1 (Jul 10, 2008)

  • Scrollbars can be adjusted manually
  • 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.

New in CLC Main Workbench 4.0 (Jun 27, 2008)

  • 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
  • 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
  • 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)

New in CLC Main Workbench 3.6.2 (Apr 10, 2008)

  • 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.

New in CLC Main Workbench 3.6.1 (Feb 28, 2008)

  • 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

New in CLC Main Workbench 3.6.1 (Feb 28, 2008)

  • 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

New in CLC Main Workbench 3.6 (Feb 12, 2008)

  • 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.

New in CLC Main Workbench 3.5.1 (Jan 8, 2008)

  • 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