CLC Main Workbench Changelog

What's new in CLC Main Workbench 7.5 Build 115026

Sep 11, 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".
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 (Sep 11, 2014)

New in CLC Main Workbench 7.0.2 (Sep 11, 2014)

New in CLC Main Workbench 7.0.1 (Sep 11, 2014)

New in CLC Main Workbench 7.0 (Sep 11, 2014)

New features and improvements:
New functionality for phylogenetic trees (was previously part of a beta plugin)
Greatly enhanced viewer for visualizing and working with phylogenetic trees. The viewer allows the user to rapidly create high-quality, publication-ready figures of the trees.
Large trees are made easy to explore using different zoom functionalities and a small minimap of the entire tree. The viewer also comes with two alternative tree layouts, namely circular layouts and radial layouts, which are great for visualizing very large trees.
Supports importing, editing and visualization of metadata associated with nodes in phylogenetic trees.
Tool to reconstruct phylogenetic trees based on k-mers. This approach avoids the computationally intensive step of constructing a multiple alignment of the input sequences. The k-mer based reconstruction tool is especially useful for whole genome phylogenetic reconstruction where the genomes are closely related.
Tool performing a statistic evaluation of different substitution models to be used with maximum likelihood tree construction. The output of this tool is a report that lists the recommended settings to be used when constructing phylogenetic trees based on maximum likelihood.
Added an option for using the Kimura 80 substitution model when creating trees with distance based methods.
Distance-based tree reconstruction methods can now reconstruct trees from protein alignments using the Jukes-Cantor substitution model or the Kimura protein ML distance estimate.
A user defined start tree can now be supplied to the ML inference tool.
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 slidershows 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. This is a great improvement which also kicks in when moving data between a CLC Genomics Server and a Workbench.
Workflows:
Possibility to have bulk configuration of elements. This enables to set the same reference data for multiple elements at once.
Workflows can be added inside a workflow. The inner workflow is "unfolded" into the single elements.
Parameters can now be renamed in the editor by the creator during configuration of the elements.
Workflows with invalid/unknown elements are laid out nicer and more consistent.
The sidepanel has now an option to display rulers in the editor to indicate better the size of a workflow (particularly when exporting)
Fit Width now fits the entire workflow in the editor by zooming out.
The sidepanel has a new section "Minimap" which shows an outline of the whole workflow. It allows to navigate the workflow in the view and also supports zooming
One can change the design of the workflow editor via the sidepanel (removed the old designs in the preferences)
Better validation when configuring parameters in workflows
If a tool receives inputs from at least two tools, the inputs can now be ordered via the context menu on the connections or the input part of the target element.
The name of an output in the workflow can be set by configuring the output element
Parameters of a workflow run can now be exported to various formats via the wizard
It is now possible to reset a reference parameter. Before it was only possible by removing the whole element and add it again.
In the workbench the installed workflows are now sorted alphabetically.
The graphics export of a workflow now knows about the scale and one can now export the whole workflow or only the current view.
A cpw file can now be dragged into the workflow manager and will be installed.
Further speed improvements on working with larger workflows in the editor
New tools that are now workflow-enabled:
All tools in Statistical Tests
3D structure viewer:
Property viewer - a new tab in the Side Panel. Shows detailed information about the atom under the mouse pointer. If multiple atoms are selected (Ctrl-click), the distance (two atoms selected), angle (three atoms selected), dihedral angle (four atoms selected) formed by the selected atoms, is shown in the Property viewer. If a molecule is selected in the Project Tree, meta-data relating to the molecule is shown in the Property viewer.
Issues List. Issues related to the molecule structures and their chemistry representation is listed in the Issues List view on Molecule Projects. If seen in split-view with the 3D viewer, a selected issue will zoom to the atoms involved in the issue and select them in the 3D view.
General improvements to the PDB importer
Double-clicking an entry in the Project Tree will zoom-to-fit on the molecule or atom group.
When selecting atoms (by mouse clicking or from sequence), the atom context (whole residue or molecule) will also be shown in the 3D view. From context menu on 'Current' selection, an atom group can be generated either from the exact selection or from the selection plus the context (whole residues or molecules).
Extract consensus sequence is now able to copy annotations from both existing consensus sequence and the reference sequence.
When extracting consensus sequence from a mapping, conflict and low coverage annotations now include the position on the reference.
Trim annotations can be used to trim off sequences when exporting to fasta.
Secondary peak calling has been improved: it now only detects peaks that have a distinct peak shape, only peaks that fall within the same interval as the top peak are called. In addition, trim annotations are taken into account so that no peaks are called within trimmed regions. This greatly reduced false positive calls. Finally, the annotations now include information about the secondary peak's fraction of the maximum peak height.
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
SignalP prediction has been updated to be server-, batch- and workflow enabled.
Folder contents view: subfolders will display how many items they have
Assemble Sequences tools now accept sequence lists as input.
REBASE restriction enzyme list updated to version 310.
Bug fixes:
Workflow:
In the editor the "Fit Width" zooming was active, but behaved as "100%" zooming. Therefore the "100%" zooming is now active instead of the "FitWidth"
Added or connected elements are now placed near where you connect or add them, even when zoomed near or far.
It was possible to Undo the action of adding a workflow output, but it was not possible to Redo afterwards.
The right-hand icons in an element now scale with zooming.
The log of a workflow run on the server contains now the same information as when run in the workbench.
When configuring elements in the editor, the "Reset to CLC Standards" button is now functional and will reset the parameters to their default values. When configuring during installation or execution the button is disabled.
The log of a server executed workflow now states when the workflow has been cancelled.
A workflow with elements which provide additional inputs could not be batched.
Crash when adding data to experiments (e.g. by running any of the statistical analysis tools) has been fixed.
Various bugs in the extract consensus sequence tool have been fixed.
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.
A problem with filtering and sorting the BLAST output table has been solved. Some of the columns were treated as text instead of numeric.
Restriction maps, histogram data, and primer tables could not be exported to csv or similar. This has been fixed.
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.
Changes:
The two tools in the "Multiplexing" folder in the toolbox category have been changed
"Process Tagged Sequences" has been removed..
"Sort Sequences by Name" has been moved directly into the Sequencing Data Analysis folder.
Motif search: annotations created by the motif search are of type "Motif" instead of "Region"

New in CLC Main Workbench 6.9.2 (Sep 11, 2014)

New in CLC Main Workbench 6.9.1 (Sep 11, 2014)

New in CLC Main Workbench 6.9 (Sep 11, 2014)

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 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.:
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” 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.
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 is 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 (Sep 11, 2014)

New in CLC Main Workbench 6.8.3 (Sep 11, 2014)

New in CLC Main Workbench 6.7.2 Build 67203 (Dec 19, 2012)

New in CLC Main Workbench 6.7.1 Build 67103 (Sep 6, 2012)

New in CLC Main Workbench 6.7 (Aug 17, 2012)

New in CLC Main Workbench 6.6.5 (Jul 26, 2012)

New in CLC Main Workbench 6.6.2 (Jul 26, 2012)

New in CLC Main Workbench 6.6.1 (Jul 26, 2012)

New in CLC Main Workbench 6.6 (Jul 26, 2012)

New in CLC Main Workbench 6.5 Build 65005 (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 Build 62011 (Oct 13, 2011)

New in CLC Main Workbench 6.1.1 Build 61103 (Jul 14, 2011)

New in CLC Main Workbench 6.1 (Jul 14, 2011)

New in CLC Main Workbench 6.0.2 (Jul 14, 2011)

New in CLC Main Workbench 6.0.1 (Jul 14, 2011)

New in CLC Main Workbench 6.0 (Jul 14, 2011)

Cloning tool re-designed to make it easier and faster to perform restriction cloning
Restriction sites used to select target vector and fragment.
Sequences can now be displayed in circular mode in the cloning editor.
Only one sequence displayed at a time (there is a list at the top of the view to switch between sequences).
Option to clone several fragments and adjust overhangs and orientation in one dialog.
New cloning tutorial available for a quick introduction.
BLAST tools have been redesigned
New Blast Database manager for easy administration and management of local BLAST databases.
More user-friendly way of creating and accessing local BLAST databases.
Much more stable design of both BLAST at NCBI and Local BLAST when running large data sets.
The SNP Annotation using BLAST tool has been discontinued.
See migration notes for using your old databases 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.
Circular view: There is a "Radial" option that will place restriction sites (and annotations) as close to the sequence as possible with a radial layout.
Improved layout of general annotations
Linear view: There is an option to separate restriction sites and annotations in separate layers.
Circular view: There is a "Radial" option that will place annotations (and restriction sites) as close to the sequence as possible with a radial layout.
Motif search available in Side Panel
Dynamic annotations will be added for motifs defined in the Side Panel (similar to restriction sites).
Use motif lists to add your own motifs to the Side Panel.
Annotation table now available for sequence lists, contigs, BLAST results and alignments.
Batching functionality available for selected tools.
Multiplexing: Process tagged sequencing data
It is now possible to import and use a file with bar codes and sample names. This makes it easier to process data with a high number of multiplexed samples.
You can specify separate output folders for each sample, making it convenient to batch process the subsequent analyses.
Support for exporting tables as tab-delimited files.
Audit option: manual editing of sequences will be recorded with an annotation on the sequence (this has to be switched on in the Preferences dialog).
The default database of restriction enzymes can be expanded (requires manual edit of database file).
The default set of codon frequencies can be expanded (requires manual edit of table files).
Improved option to export and import Side Panel settings.
Memory allocation: the default memory allocation for the Workbench changes from 75% to 50% of available physical memory with a maximum at 50 GB.
Bug fixes:
The molecular weight calculation for the sequence statistics report is more accurate and is now reported for both single- and double-stranded molecules.
Various bug-fixes

New in CLC Main Workbench 5.7.0 (Jun 16, 2010)

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

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

New features:
Expression analysis:
Volcano plots: you can now choose the values to plot on the x-axis. Choose between "Difference" and "Fold change".
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.
Gene Ontology (GO) files can now be used to annotate an expression experiment.
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.
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).
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.
Expression data importers are now described in technical details in a separate section.
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.
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.
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 unsaved data now gets a * rather than make the tab name bold and italics.

New in CLC Main Workbench 5.5.0 (Oct 9, 2009)

New in CLC Main Workbench 5.2.0 (Aug 19, 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 5.0.2 (Mar 13, 2009)

New in CLC Main Workbench 5.0.1 Build 5011 (Feb 27, 2009)

New in CLC Main Workbench 5.0 Build 5004 (Feb 4, 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 (Sep 19, 2008)

New in CLC Main Workbench 4.0 (Jun 29, 2008)

New in CLC Main Workbench 3.6.2 (Apr 15, 2008)

New in CLC Main Workbench 3.5.1 (Dec 19, 2007)

New in CLC Main Workbench 3.5 (Dec 7, 2007)

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

New in CLC Main Workbench 3.0.2.3022 (Aug 23, 2007)

New in CLC Main Workbench 3.0.1 (Jul 24, 2007)

New in CLC Main Workbench 2.2.3 (Apr 25, 2007)

New in CLC Main Workbench 2.2.2 (Mar 19, 2007)

New in CLC Main Workbench 2.2.1 (Feb 1, 2007)

New in CLC Main Workbench 2.0 (Jul 12, 2006)