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CLC DNA Workbench Changelog

What's new in CLC DNA Workbench 6.6.1

Feb 24, 2012
  • Minor improvements:
  • Translate to protein creates sequence lists as results when more than 10 sequences are produced. This greatly improves performance when translating large amounts of proteins
  • It is now possible to specify the number formatting in tables in the View Preferences.
  • Bug fixes:
  • Fixed: Downloading of protein sequences from NCBI fails.
  • Fixed: Trimming tool in Sequencing Data Analysis does not add annotation to sequences when the full sequence should be discarded.
  • Fixed: Opening external files (e.g. pdf files or Word documents) with spaces in the file name does not work on Windows.

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

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

New in CLC DNA Workbench 6.5 (Dec 16, 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: 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. The developers 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 DNA Workbench 6.2 (Oct 12, 2011)

  • New and improved features:
  • You can switch between compactness levels by pressing the Alt key while scrolling with your mouse or touchpad.
  • Translation in the Side Panel of nucleotide sequences now includes options to translate "All forward" or "All reverse" reading frames.
  • Conflict table view of read mappings: reference positions also reported in addition to the consensus sequence position.
  • Alignments: it is now possible to copy all annotations from one sequence to other sequences in the alignment.
  • Cloning editor: number of restriction cut sites and motifs are shown separately for the sequence currently displayed and for all sequences in the list.
  • Restriction enzymes updated with latest REBASE version.
  • Clean-up of the Workbench window so that it no longer holds information about which Workspace is active. This information is now displayed with check boxes in the Workspace menu.
  • Bug fixes:
  • Fixed: For circular molecules, the Find Open Reading Frames tool did not find reading frames on the negative strand. We recommend users to rerun any reading frame analyses on circular molecules.
  • Fixed: BLAST searches at NCBI always searched nr or nt, regardless of which database was specified. This has been a problem since the release of CLC DNA Workbench 6.0
  • Fixed: Pattern discovery wizard failed when the tool is run for the second time.
  • Fixed: Certain annotation types were mapped to generic annotation types when exporting sequences in Genbank format.

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

  • New and improved features:
  • All history entries will from now on include the version number of the software
  • Performance of Excel 2010 exporter improved in terms of speed and memory requirements
  • When using a license server, the Workbench user can now specify a custom user name which can be checked in the license server configuration. This makes it possible to get more fine-grained control of the users of the license server.
  • BLAST
  • BLAST parameters have been changed so that number of threads is 1 per default (there is a bug in the BLAST code provided by NCBI which makes it fails on certain data sets when using multiple threads)
  • The "Mask lower case" option has been removed
  • Tool to download BLAST databases from NCBI within the Workbench
  • Bug fixes:
  • Fixed: Alignment-based primer design failed for columns with many gaps
  • Fixed: "Find Binding Sites and Create Fragments" did not find binding sites where the primer extended the 5' end of the template sequence
  • Fixed: Import of certain special Genbank files failed
  • Various minor bug fixes

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

  • New and improved features:
  • Local BLAST is faster when blasting against small databases
  • Bug fixes:
  • Fixed: Local BLAST did not work on Mac OS 10.5
  • Fixed: Joined annotations did not get the right off set when inserting a sequence in the cloning editor.
  • Various minor bug fixes

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

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

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

  • Improvements:
  • Improved performance of table filtering. Removed limit on the number of rows that can be filtered.
  • Option to search for read names in contigs (and also sequence lists and BLAST results).
  • Improved performance of conflict table view of contigs.
  • Better layout of graphics export and printing of contigs results: reference and consensus sequence repeated to provide an orientation context on all pages.
  • Bug-fixes:
  • Fixed error when opening tables generated by the Transfac plug-in and the primer search tool
  • Fixed problem updating preview in Gateway cloning dialog
  • Genbank export of annotations on the negative strand were not in the right order
  • Fixed problems regarding editing and viewing of contigs and alignments
  • Fixed memory and performance issues related to import of many sequences, eg. from ACE files.
  • Various minor bug fixes

New in CLC DNA Workbench 5.7 (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
  • Performance of ACE export improved, especially for long reference sequences or read mapping tables.
  • Sequence annotations are packed to lower memory footprint and disk space usage, especially for SNP, DIP, and Conflict annotations.
  • Improved performance of reading data files from shared drives.
  • REBASE collection of enzymes updated to latest version
  • BLAST: In the overview BLAST table, it is now possible to extract query sequences. Read more
  • Process tagged sequences: it is now possible to input barcodes on a comma-separated list. Read more
  • Folder structure (expanded/collapsed folders) is preserved through the life-time of a wizard (e.g. when selecting input data and reference for read mapping)
  • Find in Side Panel: separators are allowed when performing position search (e.g. 1.000.000 or 1,000,000 or 1'000'000 or 1 000 000). Read more
  • New preference group called "Data" to hold information about adapter sequences and Gateway cloning primer additions. Read more
  • Bug-fixes:
  • Print of folder content now takes settings in the Side Panel into account
  • Process tagged sequences of paired data: it was not possible to specify one read without sequence (necessary for Illumina barcodes using paired data)
  • Better memory handling in conflict table
  • Find in Side Panel: space are now allowed
  • Genbank import: sequence name (LOCUS) was truncated to 18 characters

New in CLC DNA Workbench 5.7 (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
  • Performance of ACE export improved, especially for long reference sequences or read mapping tables.
  • Sequence annotations are packed to lower memory footprint and disk space usage, especially for SNP, DIP, and Conflict annotations.
  • Improved performance of reading data files from shared drives.
  • REBASE collection of enzymes updated to latest version
  • BLAST: In the overview BLAST table, it is now possible to extract query sequences. Read more
  • Process tagged sequences: it is now possible to input barcodes on a comma-separated list. Read more
  • Folder structure (expanded/collapsed folders) is preserved through the life-time of a wizard (e.g. when selecting input data and reference for read mapping)
  • Find in Side Panel: separators are allowed when performing position search (e.g. 1.000.000 or 1,000,000 or 1'000'000 or 1 000 000). Read more
  • New preference group called "Data" to hold information about adapter sequences and Gateway cloning primer additions. Read more
  • Bug-fixes:
  • Print of folder content now takes settings in the Side Panel into account
  • Process tagged sequences of paired data: it was not possible to specify one read without sequence (necessary for Illumina barcodes using paired data)
  • Better memory handling in conflict table
  • Find in Side Panel: space are now allowed
  • Genbank import: sequence name (LOCUS) was truncated to 18 characters

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

  • Opening consensus sequence including gaps will also put Ns before the consensus sequence starts and after it ends
  • Deployment:
  • You can set a path to the default data location used when the Workbench starts for the first time. This is a feature to help system administrators control where new installations per default save their data. Read more...
  • Support for removing tools accessing the internet (NCBI BLAST, update notifications etc). Read more...
  • General import and export:
  • Support for import of complex regions from GFF files
  • Export tables and reports in Excel format.
  • Import section of user manual re-structured to provide better overview. Read more.... Expression data importers are now described in technical details in a separate section. Read more....
  • You can now export multiple sequence lists in fasta format
  • Forced import of zip files is now supported (it will force import the contents of the zip file)
  • The standard import now accepts gzip and tar files as well as zip
  • If a forced import fails, there will be more technical information about what went wrong, allowing you to identify bad formatting of the import files
  • Both Genbank and gff importer now makes several attempts at naming genes that do not have a gene name. It will iteratively try the following qualifiers: "product", "locus_tag", "protein_id" and "transcript_id"
  • When importing genbank files where the length stated does not match the actual sequence, a warning is shown but the sequence is accepted.
  • When exporting in csv format, the Locale settings are used to determine whether comma or semi-colons should be used as delimiter (comma used for US locales)
  • GFF plug-in has been updated to accept complex annotations
  • Miscellaneous:
  • Advanced retyping of annotations using the annotation table. Read more...
  • Improved reporting of situations when a full disk prevents saving of data
  • Downloading sequences using drag and drop from the search table no longer creates a "Downloading..." node in the folder. The download process can be monitored in the Processes tab.
  • Primer design now supports PCR fragments longer than 5000 bp.
  • Extract Sequences moved from File manu to Toolbox-> General Sequence Analysis. Read more...
  • Better progress feedback on various dialogs
  • Bug-fixes:
  • Fixed problem displaying the "Copying..." label when copying data and then updating the folder
  • Fixed problem with naming of tabs. The fix means that on Windows and Linux unsaved data now gets a * rather than make the tab name bold and italics. (This has always been the behavior on Mac OS X).

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

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

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

  • New features:
  • Create new contig from selection
  • Import list of sequences in csv format: each line in the file represents a sequence with name, optional description, and sequence. Typically useful for importing lists of oligos.
  • Advanced view of elements in a folder including batch editing.
  • 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:
  • 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 DNA Workbench 5.1 (Jun 2, 2009)

  • New features:
  • "Reverse Contig" has been renamed to "Reverse Complement Contig." Functionality is un-changed.
  • Better feedback on processes: there is a tool tip showing details and start time.
  • Translation of DNA to protein in sequence views can now be set to follow existing CDS/ORF annotations.
  • Exporting coverage graph to csv file now has an option to include or exclude gaps. Excluding gaps will make the file use the reference sequence coordinates.
  • Much improved memory performance and processing time of large data sets.
  • Improved performance when handling trace data. Trace now take up 50 % less disk space. This means that the data is opened and saved much faster and less memory is used.
  • Output and error log files are now placed in the application data directory in the user home.
  • Bug fixes: Fixed error when parsing files from Clone Manager (cm5-files).

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

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

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

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

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

  • 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 DNA Workbench 4.1.2 (Nov 20, 2008)

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

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

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

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

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

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

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

New in CLC DNA Workbench 4.0 (Jun 26, 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 8, 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 DNA Workbench 3.6.2 (Apr 10, 2008)

  • A few bugs resolved caused by the MLST plug-in
  • BLAST of contigs no longer changes the contig name
  • Fixed issue with tooltip rendering of quality values on reversed sequencing reads
  • A few other minor bugs have been fixed.

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

  • Various bug-fixes
  • Fixed selection errors in cloning editor
  • Name of saved primers were incorrect
  • Fixed copy/paste errors in sequence list table
  • Made it possible to Ctrl-doubleclick to extend selection between restriction sites
  • Improved user interface for adding motifs to motif lists

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

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

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

  • Organism name is now available in sequence list tables.
  • Fixed Mac problem when closing tabs.
  • Fixed minor issues and improved overall program stability.
  • Improved view layout of very long sequence labels.
  • Fixed stability issues related to the Recent Items plugin.