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CLC Sequence Viewer Changelog

What's new in CLC Sequence Viewer 7.7.1

Sep 26, 2016
  • New features and improvements:
  • All NCBI server communication is now encrypted. (NCBI will be moving all web services to the HTTPS protocol on September 30, 2016).
  • The list of enzymes pre-installed in the workbench has been updated from REBASE.
  • The Quick Launch tool is now found under the Toolbox menu instead of the View menu and a button called Launch that brings up this tool has been added to the toolbar.The option "is not in list" has been introduced as a new table filtering option.
  • The "Sort folder" tool now uses numerical sorting for filenames prefixed with a number.New placeholders are available when defining the names of exporter outputs: {user}, {host}, and for elements of the timestamp of the output object, {year}, {month}, {day}, {hour, {minute}, {second}. Placeholders within export output names that were previously available only as digits can now be specified using written names: {input} is a synonym for {1}, {extension} is a synonym for {2} and {counter} is a synonym for {3}.
  • GenBank import now also allows for file names with 'GBFF' extension.
  • Read group details are now shown on the Element Info view of sequence lists.
  • Bug fixes:
  • Fixed a rare issue where some annotations could, but did not necessarily, go missing on sequences with greater than 1000 annotations of a given type on that sequence before the deletion and where the right-click context menu option "Delete selection" was used.
  • Fixed a bug in the "Manage Enzymes" wizard that prevented a user from cancelling the action if "Save as new enzyme list" was enabled.
  • Fixed an issue with the Import Metadata tool where, if a spreadsheet had already been loaded, then selecting the same spreadsheet again did not reload the spreadsheet content.
  • Fixed an issue where it took a long time to open a workbench it it was previouslyclosed when displaying an open table editor that had been sorted.
  • Fixed an issue where right-clicking on a graph in a report and choosing to show "Report", "History" or "Element Info" triggered an error.Various minor bugfixes.

New in CLC Sequence Viewer 7.7 (Mar 31, 2016)

  • NEW FEATURES AND IMPROVEMENTS:
  • Improvements:
  • All Excel sheets in a document are now imported and each sheet has a table created for its contents.
  • The CSV, HTML and Excel table/tabular exporter now use "Inf" and "NaN" values to replace the ambiguous "?".
  • In the wizard for exporting a table in CSV format, when not exporting all columns, it is now possible to cancel or go back to the previous step while selected columns are loading.
  • 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:
  • Versions of individual tools are now reported in the history of output objects.
  • Export to clc format now truncates very long filenames.
  • RPM package installers for Linux are no longer available.
  • The 'Database Fields' label shown in the 'Show Element Info' view has been renamed to ' Local Attribute Fields'.
  • The user can no longer uncheck "export all columns" for input objects that do not support this option. This applies to command line functionality as well, where the user will now receive an error if this is attempted.
  • BUG FIXES:
  • Fixed a frame offset bug that occurred when translating reverse complemented CDS regions into protein sequences.
  • The "Search for sequences at NCBI" tool would in some cases fail to download nucleotide sequences with the error message "The following sequences were not downloaded correctly: ...".
  • Fixed a bug that caused the Excel importer to use column names as cell values of the first row.
  • Fixed an issue where open tabs were not correctly ordered after splitting view horizontally or vertically using the View menu or keyboard shortcuts.
  • Fixed an issue so that double clicking on clc:// urls on Mac OS X now opens the data element in a view in an installed CLC Workbench.
  • A Workbench Data Location pointing at a file on the system instead of a folder will now appear as unavailable in the Workbench Navigation area instead of throwing an error.
  • Fixed a bug where it was possible to type non-number characters into a number field when starting up a job in the Workbench.
  • An error was previously thrown when encountering blank annotation-values. Blank values are now ignored.
  • Fixed an error that could appear when moving the mouse over annotations in a sequence annotation table.
  • Fix an issue that could lead to an error when a job status description changed while a full description was being generated.
  • Fixed an issue where, when the option to "Skip these updates" was checked in the plugin update information window, this information was not saved. This led to the same plugin update information being presented after each Workbench restart if the plugins were not updated.
  • Fixed an error that occurred when pressing the Print button in the Help dialog (Mac OS X only).
  • Fixed an issue where the text area in error dialogs did not expand vertically when the dialog was expanded.
  • Fixed a rare issue that could be triggered by switching editor view with a double click.
  • PLUGIN UPDATES AND FIXES:
  • All plugins need to installed in the new Workbench for compatibility reasons.

New in CLC Sequence Viewer 7.6.1 (Sep 8, 2015)

  • New features and improvements:
  • Tooltips on leaves of phylogenetic trees now display a description of the attached sequence.
  • One can now select "EST" as database when using the Search for Sequences at NCBI tool.
  • The output of the Reverse Complement Sequence now gets the suffix -RC attached to the name of the input instead of -1 before.
  • 3D molecule viewer improvements:
  • Molecular surfaces can now be transparent
  • A clipping plane can cut into surfaces and secondary structure
  • Options for creating atom groups and visualizing hydrogen bonds have been improved
  • Bug fixes:
  • Fixed an issue where some filtering operations, such as "doesn't contain" did not act correctly when filtering table cells that contained multiple pieces of information.
  • Fixed an issue where annotations that spanned the ends of a circular sequence would be incorrectly placed in the Circular Sequence View.
  • Fixed a bug that caused the workbench to freeze if certain sequences were displayed in circular view with radial rendering of labels.
  • Fixed an issue where some filtering operations, such as "doesn't contain" did not act correctly when filtering table cells that contained multiple pieces of information.
  • Fixed an issue that prevented a root folder on Windows drives from being used as a File Location.
  • Fixed an issue where updating an existing installation on Windows would result in the .vmoptions file being deleted, which makes the Workbench run with the default Java configuration.

New in CLC Sequence Viewer 7.6 (Feb 24, 2015)

  • New features and improvements:
  • A 3D Molecule Viewer is now available for visualization of protein, RNA, DNA, and small molecules.
  • Improved reporting of errors related to low disk space.
  • Bug fixes:
  • Fixed problem with links and text in tables that were being cut off when succeeding a link.
  • Restriction site analysis: The values "Cut position(s)" column of the restriction site analysis table now behaves like numbers instead of text, meaning sorting and filtering works.
  • A problem with saved table settings that sometimes did not work has been fixed. The bug fix includes a more robust/generic way of saving table settings with different columns. To fix this problem, existing saved table settings should first be loaded on an object where it works (i.e. has the same columns as when it was saved); and then the table settings should be saved with the old name to overwrite the settings. 
Metadata for phylogenetic trees: A bug has been fixed with import of metadata containing column names with colons. 
Fixed error when showing protein translations of annotations shorter than 3 bases.

New in CLC Sequence Viewer 7.5 (Sep 6, 2014)

  • New features and improvements:
  • The unused "Workflows" button has been removed from the toolbar.
  • Local Search enabled from the menu bar now includes filtering on "Path".
  • Advanced filtering on tables now includes the option to filter for a space, comma or semi-colon delimited lists of terms.
  • Zoom tools redesign: The “Zoom to selection” feature is now also available for sequences, sequence lists, alignments, and read mappings.
  • Saving/applying side-panel settings for tables now works for different tables that share some columns.
  • Copy operations can now be stopped.
  • Import of Example Data and imports done through dragging files into the workbench and dropping them in the Navigation Area will no longer block the user interface while executing. Instead, the import happens as a background process that can be monitored and controlled via the Processes tab in the lower left corner.
  • CLC workbenches now support high resolution displays such as Apple retina displays of all data shown in the View Area (including tooltips).
  • More informative naming of coding region translations produced by the tool Translate to Protein. The name for a coding region translation consists of the name of the input sequence followed by the annotation type and finally the annotation name.
  • 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 Sequence Viewer 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 Sequence Viewer 7.0.1 (Mar 17, 2014)

  • Fasta export now reports progress while executing
  • 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
  • Bug fixes:
  • Fixed missing icon for "Metadata Import" in the phylogenetic tree table

New in CLC Sequence Viewer 7.0.0 (Feb 11, 2014)

  • Complete redesign of the graphical user interface including:
  • New tool bar graphics
  • New product logos and colors, including splash screen
  • New background graphics on canvas and in dialogs
  • Tool bar has been re-organized
  • New tab design. Aligning the look and feel across platforms, which is particularly important to mac-users as split screen used to take up a lot of screen space.
  • New concept for Side Panels and Views:
  • Support for multiple screens: views can be moved to a different screen by dragging the tab of the view
  • Side Panels now consist of palettes that can be organized in group and the order can be customized
  • Palettes can be detached and placed anywhere on the screen
  • Navigation Area and Toolbox can be minimized to allow more pixels for displaying data
  • Zoom tools redesign:
  • The zoom tools have been re-organized and placed closer to the data
  • A zoom slider shows the present zoom level and can be used to adjust zoom
  • Detailed zoom is a new feature that allows zooming in and out in very small increments by dragging the zoom slider and moving the cursor above it. An expert feature for e.g. large tracks.
  • New zoom tools. Easy adjustment of zoom speed for improved zooming of huge sequences.
  • Detachable Side Panel editors. A Side Panel editor can be dragged from the main workbench window and dropped outside the workbench, making a separate window e.g. on a second screen, if available.
  • Copying data in the Navigation Area runs much faster and uses less memory than before.
  • Advanced table filter now includes an option to search for "starts with" in addition to just "contains"
  • Limitations on export of Excel 2010 files (xlsx) are removed:
  • Multiple tables can be exported to one xlsx file
  • Reports can be exported to xlsx
  • Hyperlinks are preserved in xlsx files
  • Folder contents view: subfolders will display how many items they have
  • REBASE restriction enzyme list updated to version 310.
  • Bug fixes:
  • When translating to protein, ambiguous nucleotides potentially resulting in stop codons were not translated properly, and only the codons resulting in an amino acid were represented in the protein. Now the stop codons are also represented by an X in the protein sequence.
  • When using the “Find Open Reading Frame” tool, the input sequence was reported incorrectly in the ORF table. This has been fixed.
  • Fixed problems with Excel export that failed when special characters were used in the name.

New in CLC Sequence Viewer 6.9.1 (Oct 24, 2013)

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

New in CLC Sequence Viewer 6.9 (Jul 22, 2013)

  • New features:
  • Export framework redesigned:
  • Export of multiple files: you can export several files in one go. The naming of the file will default to the name used in the Navigation Area of the Workbench, but the user can specify a naming pattern to use instead.
  • Export formats: A new column “Exports selected” has been added to the “Select exporter” table that indicates with a “Yes”, “No” or “Partly” whether the currently selected element can be exported with the given exporters. Partly means that you have made a selection of elements where only some of them can be exported by the selected exporter.
  • Improved usability with a quick-select dialog for choosing the right export format. The dialog includes a description of each exporter that can be quickly filtered.
  • Export can be integrated into workflows
  • Support for direct compression of exported files in zip and gzip.
  • The folder 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.:
  • 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.
  • Improvements:
  • When using the “Translate to protein” tool, the max limit has been raised to 1GB.
  • The sequence action "Open Copy" has been removed and "Open This Sequence" has been renamed to "Open Sequence".
  • Renaming of data in the Navigation Area by clicking twice has been improved. Previously, you could accidentally enter rename mode when the intention was to get focus in the Navigation Area. Now, you can only trigger rename by clicking when the Navigator has focus.
  • The alignment tool is now more memory efficient.
  • Tables: Improved auto-adjustment of the column width (based on content and number of columns).
  • Usability improvement of simple table filtering:
  • A dedicated filter button has been added to apply the filter directly without having to wait until the filter is automatically applied
  • For tables with more than 10000 rows, the filter will not be applied automatically after a delay. Instead, there is a helping text asking the user to apply the filter through the "Filter" button. This avoids premature filtering before entry of the filter text has completed. Since filter can take some seconds for large tables, this used to be an annoyance because the user would have to wait until filtering was done to complete the entry.
  • Bug fixes:
  • PDF export of the history of a result did not include the name and version number of the Workbench that produced the result.
  • Changes:
  • System requirements for Linux has changed. From this release, SuSE is supported from version 10.2. This was previously version 10.0

New in CLC Sequence Viewer 6.8.2 (Apr 3, 2013)

  • Improvements:
  • For alignments, sequence lists and other sequence views, the right-click options to Open Copy of Sequence and Open This Sequence have been merged to Open Sequence. If a copy should be created, use Save As with the new sequence, or drag it into a folder in the Navigation Area.
  • Bug fixes:
  • 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 Sequence Viewer 6.8.1 (Jan 31, 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 Sequence Viewer 6.7.1 (Sep 7, 2012)

  • Various bug fixes

New in CLC Sequence Viewer 6.7 (Aug 10, 2012)

  • 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
  • A new translation table added: Pterobranchia mitochondrial (see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG24)

New in CLC Sequence Viewer 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 Sequence Viewer 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: Opening external files (e.g. pdf files or Word documents) with spaces in the file name does not work on Windows.

New in CLC Sequence Viewer 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.

New in CLC Sequence Viewer 6.5.4 (Nov 29, 2011)

  • New and improved features:
  • Exporting fastq format no longer includes redundant name of the read in the quality score line. Now the name only appears once per read.
  • Bug fixes:
  • Fixed: Annotations spanning the sequence from start to end did not display right when the sequence was wrapped. The annotation was only displayed on the first line.

New in CLC Sequence Viewer 6.5.3 (Oct 12, 2011)

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

New in CLC Sequence Viewer 6.5.1 (Jun 22, 2011)

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

New in CLC Sequence Viewer 6.5.0 (Jan 26, 2011)

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

New in CLC Sequence Viewer 6.4.0 (Jun 16, 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
  • Sequence annotations are packed to lower memory footprint and disk space usage, especially for SNP, DIP, and Conflict annotations.
  • Improved performance of reading data files from shared drives.
  • Folder structure (expanded/collapsed folders) is preserved through the life-time of a wizard (e.g. when selecting input data and reference for read mapping)
  • Find in Side Panel: separators are allowed when performing position search (e.g. 1.000.000 or 1,000,000 or 1'000'000 or 1 000 000). Read more
  • Bug-fixes:
  • Print of folder content now takes settings in the Side Panel into account
  • Find in Side Panel: space are now allowed
  • Genbank import: sequence name (LOCUS) was truncated to 18 characters

New in CLC Sequence Viewer 6.3.0 (Dec 15, 2009)

  • New features:
  • Deployment
  • You can set a path to the default data location used when the Workbench starts for the first time. This is a feature to help system administrators control where new installations per default save their data. Read more...
  • Support for removing tools accessing the internet (NCBI search, update notifications etc). Read more...
  • General import and export:
  • Export tables and reports in Excel format.
  • Import section of user manual re-structured to provide better overview. Read more.... Expression data importers are now described in technical details in a separate section. Read more....
  • You can now export multiple sequence lists in fasta format
  • Forced import of zip files is now supported (it will force import the contents of the zip file)
  • The standard import now accepts gzip and tar files as well as zip
  • If a forced import fails, there will be more technical information about what went wrong, allowing you to identify bad formatting of the import files
  • Both Genbank and gff importer now makes several attempts at naming genes that do not have a gene name. It will iteratively try the following qualifiers: "product", "locus_tag", "protein_id" and "transcript_id"
  • When importing genbank files where the length stated does not match the actual sequence, a warning is shown but the sequence is accepted.
  • When exporting in csv format, the Locale settings are used to determine whether comma or semi-colons should be used as delimiter (comma used for US locales)
  • Miscellaneous:
  • Improved reporting of situations when a full disk prevents saving of data
  • Downloading sequences using drag and drop from the search table no longer creates a "Downloading..." node in the folder. The download process can be monitored in the Processes tab.
  • Extract Sequences moved from File menu to Toolbox-> General Sequence Analysis. Read more...
  • Better progress feedback on various dialogs
  • 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 Sequence Viewer 6.2.0 (Aug 18, 2009)

  • New features:
  • Import list of sequences in csv format: each line in the file represents a sequence with name, optional description, and sequence. Typically useful for importing lists of oligos.
  • Advanced view of elements in a folder including batch editing.
  • Extract sequences improvements
  • You can now drag results from NCBI searches into the view area to open directly (previously you could only drag into a folder to save)
  • "Find" in text view now accepts Enter as command to find the next hit
  • Importing VectorNTI archives previously resulted in a sequence list. Now it imports as single sequences.
  • Export of annotations in GFF format (note that annotations with joined regions are not supported)
  • Bug fixes:
  • Problem rendering scatter plots without lines
  • DNA strider files could loose name upon import
  • Rare misplacement of annotations when editing very large sequences
  • Various bug-fixes

New in CLC Sequence Viewer 6.1 (Jun 2, 2009)

  • New features:
  • Better feedback on processes: there is a tool tip showing details and start time.
  • Much improved memory performance and processing time of large data sets.
  • Output and error log files are now placed in the application data directory in the user home.
  • Bug fixes:
  • Fixed error when parsing files from Clone Manager (cm5-files).

New in CLC Sequence Viewer 6.0.2 (Mar 12, 2009)

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

New in CLC Sequence Viewer 6.0.1 (Feb 27, 2009)

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

New in CLC Sequence Viewer 6.0 (Jan 28, 2009)

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

New in CLC Sequence Viewer 5.1.2 (Nov 20, 2008)

  • The Side Panel's Find only high-lighted the first hit. This is now fixed.
  • Better performance when zooming a dot plot.
  • Better performance when using the Side Panel's Find in large contigs and sequence lists.
  • Multi-select (using Ctrl / Command key) did not work for sequence lists.
  • Various bug fixes.

New in CLC Sequence Viewer 5.1.1 (Oct 2, 2008)

  • Fixed problems when scrolling very large sequences.
  • Fixed problem when importing very large GenBank files.

New in CLC Sequence Viewer 5.1 (Sep 18, 2008)

  • Improved performance when handling large data sets.
  • Various bug-fixes.

New in CLC Sequence Viewer 5.0.1 (Jul 10, 2008)

  • Scrollbars can be adjusted manually
  • Fixed problems when aligning sequences with lowercase characters
  • Fixed import of trace files without quality scores
  • A new sequence list can be created from a selection in the table view
  • User definable scrollbar areas for contig views
  • A few other minor bugs have been fixed.

New in CLC Sequence Viewer 5.0 (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
  • 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 Sequence Viewer 4.6.2 (Apr 10, 2008)

  • A few minor bugs have been fixed.

New in CLC Sequence Viewer 4.6.1 (Feb 29, 2008)

  • CLC Free Workbench is now called CLC Sequence Viewer.
  • Various bug-fixes
  • Fixed copy/paste errors in sequence list table
  • Made it possible to Ctrl-doubleclick to extend selection between restriction sites

New in CLC Sequence Viewer 4.5.1 (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.

New in CLC Sequence Viewer 4.5 (Dec 7, 2007)

  • Framework
  • New and improved plug-in and resource management
  • New user interface
  • Quick button in toolbar
  • Better progress measurement during download, installation etc.
  • Automatic update check
  • Automatic restart (after plug-in installation, exceeding of memory capacity and license changes)
  • Views
  • Copying work better in both sequence viewers and tables (no need to right-click any more)
  • Position of annotations in alignments etc. now relative to both alignment and sequence
  • Selecting a row in a table makes an interactive selection on the corresponding sequence (now implemented for all relevant tables)
  • The Find functionality in the Side Panel has been improved to make it possible to search in sequences with ambiguity character e.g. Ns
  • It is possible to open much larger sequence lists in the graphical view.
  • Restriction sites
  • Side Panel re-design
  • Sorting of enzymes by alphabet, number of cuts or overhang type
  • Simpler management of enzymes
  • Improved tool tips on side panel enzymes showing recognition sequence and cleavage pattern
  • Quickjump to restriction sites
  • Improved enzyme selection wizard
  • Tool tips on restriction sites now include:
  • Methylation inhibition
  • Possible star activity (non-specific recognition and cleavage)
  • Enzyme list table:
  • Information about possible star activity (non-specific recognition and cleavage)
  • New button: Add/Remove Enzymes
  • New button: Create new enzyme list from selection
  • Miscellaneous
  • Shuffle sequence includes more algorithms - now possible to shuffle while preserving di-nucleotide frequency
  • Added codon frequency tables for: *Arthrobacter aurescens TC1 *Streptomyces coelicolor A3(2)
  • Finding open reading frames: the table includes more information:
  • Strandedness
  • Nucleotides in the start codon
  • It is now possible to extract all sequences from a sequence list, an alignment or a contig (File->Extract Sequences)
  • Plug-ins
  • Sequence reader - reads sequence aloud
  • Recent items - show updated list of recently used data
  • VNTI import - including import of VNTI archives
  • Example data
  • Example data is included in the installation file - no need for download
  • Large vector library included
  • New RNA sequences