Softpedia >Windows >Science / CAD >CLC Sequence Viewer >  Changelog

CLC Sequence Viewer Changelog

What's new in CLC Sequence Viewer 8.0 Build 168747

Feb 19, 2018
  • Improvements and changes:
  • The history of a data element can now be exported as a CSV format file.
  • Fixed an issue where data exported with gzip or zip compression did not have the .gz or .zip suffix appended to the filename when earlier exports had been made with the same name and export location specified.
  • The GCG sequence exporter has been removed. The GCG alignment exporter is unaffected by these changes.
  • HTML formatting tags are now removed during export of data to Excel .xlsx or .xls format. This change does not affect the export of hyperlinks.
  • The Search for Sequences at NCBI tool now uses accession.version identifiers instead of GI numbers, as GI numbers are being phased out by NCBI (see https://ncbiinsights.ncbi.nlm.nih.gov/2016/07/15/ncbi-is-phasing-out-sequence-gis-heres-what-you-need-to-know/.)
  • In table views, it is now possible to filter columns with the filters "Is in list" and "Is not in list" when the values are numbers.
  • The help window can now be closed by pressing the escape key.
  • The "Help" and "Reset" buttons in pop-up dialogs are now buttons with text labels. They were previously buttons with icons.
  • All wizard steps are now shown in the wizard sidebar when starting a tool or workflow.
  • Various minor improvements.
  • Bug fixes:
  • Fixed an issue where filtering a log for a job that was still running would result in error dialogs.
  • Fixed an issue where a warning message about paired reads was incorrectly displayed when creating a new Sequence List with single end reads and an odd number of sequences.
  • Fixed a bug where a cell containing multiple hyperlinked URLs caused export to Excel 2010 or Excel 97-2007 format to fail. Such cell contents are now written in plain text.
  • Various minor bugfixes.

New in CLC Sequence Viewer 6.8.1 Build 68101 (Jan 30, 2013)

  • Improvements:
  • Added Legal and Tabloid formats for printing
  • Bug fixes:
  • Fixed an error when translating DNA to protein. When more than 10 sequences were produced, the resulting protein sequence included X instead of * as stop symbol. We advice customers to re-run any analyses with the translation tool when using more than 10 sequences as input.
  • Various minor bug-fixes

New in CLC Sequence Viewer 6.8 (Jan 30, 2013)

  • New features:
  • Toolbox improvements:
  • New Favorite Toolbox: A new tab next to the Toolbox holds
  • Frequently used tools. This is automatically updated based on which tools are used most frequently.
  • Favorite tools: Right-clicking a tool in the Toolbox allows you to add a tool to your favorites list.
  • Quick launch of tools: Pressing Ctrl + Shift + T shows a dialog for easy typing and launching tools.
  • Relevant view settings are now copied when switching between different views of the same data. As an example: if you have specified a set of restriction enzymes to display in the circular view of a sequence and switch to the linear view, these enzymes will also be listed in the Side Panel here. Note that the Side Panel settings are only copied to the new view if they have been changed by the user in the old view.
  • Performance when sorting of large tables has been improved
  • Rename can now be done through right-click menu in Navigation Area.
  • Annotations on circular sequences:
  • When shown in linear view they have a cleaner appearance. Before, there was a line from beginning to end of the annotation, and this has now been removed.
  • When shown in circular view, it is no longer displayed as a joined annotation over the start point but as a continuous annotation.
  • Alignments: The performance of the algorithm for running multiple alignments has been improved and now runs on multiple cores.
  • Find Open Reading Frames can be run in batch and workflows
  • Translate to protein can be run in batch and workflows
  • Restriction map: Excel export now creates a sheet for both the cut sites table and the restriction map.
  • Export now has progress and can be canceled.
  • Shortcut key for Translate to Protein has changed from Ctrl + Shift + T into Ctrl + Shift + P.
  • Bug fixes:
  • Fixed problem of not correctly formatting qualifiers in EMBL export.
  • Fixed a problem sorting sequence lists on modification date.
  • Various bug fixes.

New in CLC Sequence Viewer 6.7 (Aug 17, 2012)

  • Improvements:
  • It is possible to create sequence lists based on other sequence lists (not only single sequences)
  • Listing folder elements in the Navigation Area is faster
  • Translate to protein creates sequence lists when there are more than ten sequences
  • A new translation table added: Pterobranchia mitochondrial (see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG24)

New in CLC Sequence Viewer 6.6.2 (Aug 17, 2012)

  • Improvements:
  • Aligned fasta import and export is now supported (see http://www.bioperl.org/wiki/FASTA_multiple_alignment_format). A consequence of this is that the standard fasta import of sequences will reject to import sequences that contain gaps, assuming they should be imported as alignments instead.

New in CLC Sequence Viewer 6.6.1 (Aug 17, 2012)

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

New in CLC Sequence Viewer 6.6 (Aug 17, 2012)

  • New plug-ins and plug-in updates:
  • Additional Alignments Plug-in updated
  • The algorithms have been updated to the most recent versions
  • The list of algorithms has been reduced to two for compatibility reasons
  • New and improved features:
  • Printing and pdf export of assemblies: the assemblies are now wrapped to make better use of the paper.
  • Usability of Close icon on tabs has been improved. Both in terms of responsiveness and making it impossible by accident to initiate a drag and drop movement when you hit the close icon to try to close a tab.
  • "Show" submenu has been removed from File Menu, and the right-click menu now includes only the relevant views and editors. This provides a better overview.
  • The behavior of the Close Other Tabs function has changed so that it will close all views, regardless of the way the view area is split.
  • The most common annotation types are assigned a special color per default. Other annotation types previously got the same color. This has been extended so that the Workbench attempts to find a special color for each type.

New in CLC Sequence Viewer 6.5.4 (Aug 17, 2012)

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

New in CLC Sequence Viewer 6.5.3 Build 65311 (Oct 13, 2011)

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

New in CLC Sequence Viewer 6.5.1 (Jul 14, 2011)

  • Improved support for systems with 512 MB of memory or less

New in CLC Sequence Viewer 6.5.0 (Jul 14, 2011)

  • 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.
  • Annotation table now available for sequence lists and alignments.
  • 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).
  • 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.
  • The molecular weight calculation for the sequence statistics report is more accurate and is now reported for both single- and double-stranded molecules.

New in CLC Sequence Viewer 6.4.0 (Jun 16, 2010)

  • New features:
  • Improved memory management in general: lower memory footprint and shorter management overhead pauses.
  • Improved memory handling of large tabular data sets.
  • Improved consistency of data handling including faster listing of folder contents
  • Performance when saving small files significantly improved
  • Sequence annotations are packed to lower memory footprint and disk space usage, especially for SNP, DIP, and Conflict annotations.
  • Improved performance of reading data files from shared drives.
  • Folder structure (expanded/collapsed folders) is preserved through the life-time of a wizard (e.g. when selecting input data and reference for read mapping)
  • Find in Side Panel: separators are allowed when performing position search (e.g. 1.000.000 or 1,000,000 or 1'000'000 or 1 000 000). Read more
  • Bug-fixes:
  • Print of folder content now takes settings in the Side Panel into account
  • Find in Side Panel: space are now allowed
  • Genbank import: sequence name (LOCUS) was truncated to 18 characters

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

  • New features:
  • Deployment:
  • You can set a path to the default data location used when the Workbench starts for the first time. This is a feature to help system administrators control where new installations per default save their data. Read more...
  • Support for removing tools accessing the internet (NCBI search, update notifications etc).
  • General import and export:
  • 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)
  • Miscellaneous:
  • Improved reporting of situations when a full disk prevents saving of data
  • Downloading sequences using drag and drop from the search table no longer creates a "Downloading..." node in the folder. The download process can be monitored in the Processes tab.
  • Extract Sequences moved from File menu to Toolbox-> General Sequence Analysis.
  • 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.

New in CLC Sequence Viewer 6.2.0 (Aug 19, 2009)

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

New in CLC Sequence Viewer 6.0.2 (Mar 13, 2009)

  • Better performance of files with many annotations
  • Fixed error and improved performance of Join Sequences tool

New in CLC Sequence Viewer 6.0.1 Build 6011 (Feb 27, 2009)

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

New in CLC Sequence Viewer 6.0 Build 6003 (Feb 4, 2009)

  • Improved user experience of processes
  • Non-modal feedback from processes:
  • When there is a message
  • If you have chosen to save the results in the last step of the wizard, you will be notified when the process is done.
  • Processes running on the CLC Science Server will notify when they are done.
  • Possibility to open results by clicking the button next to the process
  • Possibility to find and select results in the Navigation Area by clicking the button next to the process
  • You can see a log of your process by clicking the button next to the process (even if you did not choose to see the log in the last step of the wizard)
  • General improvements
  • 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
  • More elaborate error reports including error logs
  • You can specify which folder the Workbench should use for temporary files
  • Extract sequences from a sequence list, contig or alignment by right-clicking the white empty space. You will then be able to extract the sequences into a list or as separate sequences.
  • The "Find" option in the Side Panel of sequence views automatically detects if you have entered a position instead of a sequence.
  • Bug fixes
  • Locale settings were not automatically set right on the first start-up. The locale settings determine whether . or , should be used for before decimals. For new installations of the Workbench, it will now be set to the locale of the computer's operating system. For existing installations, you will have to change this in the Edit->Preferences dialog.
  • Various performance improvements and bug fixes

New in CLC Sequence Viewer 4.5.1 (Dec 19, 2007)

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

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

  • New and improved plug-in and resource management
  • New user interface
  • Quick button in toolbar
  • Better progress measurement during download, installation etc.
  • Automatic update check
  • Automatic restart (after plug-in installation, exceeding of memory capacity and license changes)
  • Copying work better in both sequence viewers and tables (no need to right-click any more)
  • Position of annotations in alignments etc. now relative to both alignment and sequence
  • Selecting a row in a table makes an interactive selection on the corresponding sequence (now implemented for all relevant tables)
  • The Find functionality in the Side Panel has been improved to make it possible to search in sequences with ambiguity character e.g. Ns
  • It is possible to open much larger sequence lists in the graphical view.
  • Side Panel re-design
  • Sorting of enzymes by alphabet, number of cuts or overhang type
  • Simpler management of enzymes
  • Improved tool tips on side panel enzymes showing recognition sequence and cleavage pattern
  • Quickjump to restriction sites
  • Improved enzyme selection wizard
  • Tool tips on restriction sites now include:
  • Methylation inhibition
  • Possible star activity (non-specific recognition and cleavage)
  • Enzyme list table:
  • Information about possible star activity (non-specific recognition and cleavage)
  • New button: Add/Remove Enzymes
  • New button: Create new enzyme list from selection
  • 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)
  • Creating phylogenetic trees is done 10 times faster that before
  • Creating pairwise comparison tables is done 10 times faster that before
  • 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 Sequence Viewer 4.0.3 (Oct 8, 2007)

  • Better import of aln files
  • Solved problem with annotation rendering when inserting long sequences
  • Annotation labels are now appended when exporting into GenBank format

New in CLC Sequence Viewer 4.0.2.4022 (Aug 23, 2007)

  • The following has been updated: A few help updates. Better detection of memory on computers with more than 2 GB RAM. Better license handling on Windows Vista. Fixed error in alignment editing. Improved program stability. Improved ORF detection on negative strands of circular molecules. Better file naming when importing raw sequence data.

New in CLC Sequence Viewer 4.0.2 (Aug 23, 2007)

  • A few help updates
  • Better detection of memory on computers with more than 2 GB RAM
  • Better license handling on Windows Vista
  • Fixed error in alignment editing
  • Improved program stability
  • Improved ORF detection on negative strands of circular molecules
  • Better file naming when importing raw sequence data

New in CLC Sequence Viewer 3.0.1 (Jul 20, 2006)

  • Some of the improvements are: Nexus parser fully functional, Bootstrap values visible bug fixed, Alignment gap-cost overflow management, Cut/delete in navigator improved, Even more user-friendly import-dialog, Atom-count in sequence statistics bug fixed, Attempting to drag more than 100 sequences no longer opens viewers, Improved import of nucleotides from Vector NTI, Import of oligos from Vector NTI

New in CLC Sequence Viewer 2.5.2 (Apr 20, 2006)

  • Free choice of bootstrap replicates when inferring phylogenetic trees
  • Option of canceling graphics export processes
  • When sequences are opened, they are now zoomed to nucleotide level per default
  • A number of bug-fixes