New features and improvements
- The unused "Workflows" button has been removed from the toolbar.
- Local Search enabled from the menu bar now includes filtering on "Path".
- Advanced filtering on tables now includes the option to filter for a space, comma or semi-colon delimited lists of terms.
- Zoom tools redesign: The “Zoom to selection” feature is now also available for sequences, sequence lists, alignments, and read mappings.
- Saving/applying side-panel settings for tables now works for different tables that share some columns.
Copy operations can now be stopped.
Import of Example Data and imports done through dragging files into the workbench and dropping them in the Navigation Area will no longer block the user interface while executing. Instead, the import happens as a background process that can be monitored and controlled via the Processes tab in the lower left corner.
- CLC workbenches now support high resolution displays such as Apple retina displays of all data shown in the View Area (including tooltips).
- More informative naming of coding region translations produced by the tool Translate to Protein. The name for a coding region translation consists of the name of the input sequence followed by the annotation type and finally the annotation name.
- Due to upgrade to Java 7, Windows Server 2003 and OSX 10.5.8, 10.6 are no longer supported by Oracle. Hence, the system requirements are now: Linux, Windows Vista, Windows 7, Windows 8 or Windows Server 2008, or Mac OS X 10.7 or later.
- Fixed problems causing an error when trying to uninstall plugins.
- Fixed issue with pausing and resuming running processes
New features and improvements
- Translate to Protein (Batch Process):
- The wizard now has options for specifying whether to translate the coding regions or extract translations from the annotations
- The log has been made more detailed and informative
- If the result is just a single protein sequence, the output will be just that, otherwise all sequences are output as a list
- If the tool estimates that the number of protein sequences to be produced is greater than 1.000.000, it will create protein sequences without history, and it will not copy the common name, latin name, and taxonomy fields
Fasta export now reports progress while executing
- Fixed missing icon for "Metadata Import" in the phylogenetic tree table
New features and improvements
Complete redesign of the graphical user interface including:
- New tool bar graphics
- New product logos and colors, including splash screen
- New background graphics on canvas and in dialogs
- Tool bar has been re-organized
- New tab design. Aligning the look and feel across platforms, which is particularly important to mac-users as split screen used to take up a lot of screen space.
- New concept for Side Panels and Views:
- Support for multiple screens: views can be moved to a different screen by dragging the tab of the view
- Side Panels now consist of palettes that can be organized in group and the order can be customized
- Palettes can be detached and placed anywhere on the screen
- Navigation Area and Toolbox can be minimized to allow more pixels for displaying data
- Zoom tools redesign:
- The zoom tools have been re-organized and placed closer to the data
- 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.
- 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.
- 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.
- Fixed: GFF export failed.
- Fixed: Copying information from the Folder Contents view did not work.
- Export framework redesigned
- Export of multiple files: you can export several files in one go. The naming of the file will default to the name used in the Navigation Area of the Workbench, but the user can specify a naming pattern to use instead.
Export formats: A new column “Exports selected” has been added to the “Select exporter” table that indicates with a “Yes”, “No” or “Partly” whether the currently selected element can be exported with the given exporters. Partly means that you have made a selection of elements where only some of them can be exported by the selected exporter.
- Improved usability with a quick-select dialog for choosing the right export format. The dialog includes a description of each exporter that can be quickly filtered.
- Export can be integrated into workflows
- Support for direct compression of exported files in zip and gzip.
- The folder view has been improved with the following:
- It is now possible to drag and drop objects from the folder editor. This will create a copy of the objects at the selected destination.
- Attribute columns will be left empty if the attribute has not been defined (previously attribute values that had not been defined were set to 0 and checkboxes were shown as unchecked).
- A new column showing the first 50 residues of each sequence has been added as an option.
- The column with the name “Length” has been renamed to “Size”.
- The column “Size” shows the length of a sequence, or for sequence lists, the number of sequences e.g.:
- Alignments: the length of the alignment
- The Side Panel “Save/Restore Settings” function has been expanded with a new feature:
The “Save/Restore Settings” function (found at the top of the Side Panel) has been redesigned. It is now possible to save settings in two different ways. 1) The settings can be saved for this element type in general, e.g. for a track it would be save settings “For Track View in General”. In this way the settings will be applied each time you open an element of the same type, which in this case means each time one of the saved tracks are opened from the Navigation Area, these settings will be applied. These “general” settings are user specific and will not be saved with or exported with the element. 2) Settings can be saved with the specific element only e.g. for a track it would be save settings “On This Track Only”. The settings are saved with only this element (and will be exported with the element if you later select to export the element to another destination).
Alignments: If you have one particular sequence that you would like to use as a reference sequence, it can be useful to move this to the top. This can now be done automatically by right clicking on the sequence name and then selecting “Move Sequence to Top ”.
- The Sequence List Table has been improved with a new feature. A new column showing the first 50 residues of each sequence has been added as an option.
- When using the “Translate to protein ” tool, the max limit has been raised to 1GB.
The sequence action "Open Copy" has been removed and "Open This Sequence" has been renamed to "Open Sequence ".
- Renaming of data in the Navigation Area by clicking twice has been improved. Previously, you could accidentally enter rename mode when the intention was to get focus in the Navigation Area. Now, you can only trigger rename by clicking when the Navigator has focus.
- The alignment tool is now more memory efficient.
- Tables: Improved auto-adjustment of the column width (based on content and number of columns).
- Usability improvement of simple table filtering :
- A dedicated filter button has been added to apply the filter directly without having to wait until the filter is automatically applied
- For tables with more than 10000 rows, the filter will not be applied automatically after a delay. Instead, there is a helping text asking the user to apply the filter through the "Filter" button. This avoids premature filtering before entry of the filter text has completed. Since filter can take some seconds for large tables, this used to be an annoyance because the user would have to wait until filtering was done to complete the entry.
- PDF export of the history of a result did not include the name and version number of the Workbench that produced the result.
- System requirements for Linux has changed. From this release, SuSE is supported from version 10.2. This was previously version 10.0
- 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.
- Added Legal and Tabloid formats for printing
- 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
- 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.
- New Favorite Toolbox: A new tab next to the Toolbox holds
- Relevant view settings are now copied when switching between different views of the same data. As an example: if you have specified a set of restriction enzymes to display in the circular view of a sequence and switch to the linear view, these enzymes will also be listed in the Side Panel here. Note that the Side Panel settings are only copied to the new view if they have been changed by the user in the old view.
- Performance when sorting of large tables has been improved
- Rename can now be done through right-click menu in Navigation Area.
- Annotations on circular sequences:
- When shown in linear view they have a cleaner appearance. Before, there was a line from beginning to end of the annotation, and this has now been removed.
- When shown in circular view, it is no longer displayed as a joined annotation over the start point but as a continuous annotation.
- Alignments: The performance of the algorithm for running multiple alignments has been improved and now runs on multiple cores.
- Find Open Reading Frames can be run in batch and workflows
- Translate to protein can be run in batch and workflows
- Restriction map: Excel export now creates a sheet for both the cut sites table and the restriction map.
- Export now has progress and can be canceled.
- Shortcut key for Translate to Protein has changed from Ctrl + Shift + T into Ctrl + Shift + P.
- Fixed problem of not correctly formatting qualifiers in EMBL export.
- Fixed a problem sorting sequence lists on modification date.
- Various bug fixes.
- Various bug fixes
- 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)
- 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.
- 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.
- 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.
You can view older releases in our CLC Sequence Viewer release archive.