CLC Sequence Viewer

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CLC Sequence Viewer
Software Details:
Version: 7.7.1 updated
Upload Date: 1 Oct 16
Developer: CLC bio
Distribution Type: Freeware
Downloads: 35
Size: 71872 Kb

Rating: 0.0/5 (Total Votes: 0)

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CLC Sequence Viewer creates a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, and excellent graphical viewing and output options.

What is new in this release:

New features and improvements

  • All NCBI server communication is now encrypted. (NCBI will be moving all web services to the HTTPS protocol on September 30, 2016). 

  • The list of enzymes pre-installed in the workbench has been updated from REBASE.

  • The Quick Launch tool is now found under the Toolbox menu instead of the View menu and a button called Launch that brings up this tool has been added to the toolbar.

  • The option "is not in list" has been introduced as a new table filtering option.
  • The "Sort folder" tool now uses numerical sorting for filenames prefixed with a number.

  • New placeholders are available when defining the names of exporter outputs:  {user}, {host}, and for elements of the timestamp of the output object, {year}, {month}, {day}, {hour, {minute}, {second}. 
  • Placeholders within export output names that were previously available only as digits can now be specified using written names: {input} is a synonym for {1}, {extension} is a synonym for {2} and {counter} is a synonym for {3}.
  • GenBank import now also allows for file names with 'GBFF' extension.

  • Read group details are now shown on the Element Info view of sequence lists.

Bug fixes

  • Fixed a rare issue where some annotations could, but did not necessarily, go missing on  sequences with greater than 1000 annotations of a given type on that sequence before the deletion and where the right-click context menu option "Delete selection" was used. 

  • Fixed a bug in the "Manage Enzymes" wizard that prevented a user from cancelling the action if "Save as new enzyme list" was enabled.

  • Fixed an issue with the Import Metadata tool where, if a spreadsheet had already been loaded, then selecting the same spreadsheet again did not reload the spreadsheet content.

  • Fixed an issue where it took a long time to open a workbench it it was previouslyclosed when displaying an open table editor that had been sorted. 

  • Fixed an issue where right-clicking on a graph in a report and choosing to show "Report", "History" or "Element Info" triggered an error.

  • Various minor bugfixes.

What is new in version 7.7:

  • All Excel sheets in a document are now imported and each sheet has a table created for its contents.
  • The CSV, HTML and Excel table/tabular exporter now use "Inf" and "NaN" values to replace the ambiguous "?".
  • In the wizard for exporting a table in CSV format, when not exporting all columns, it is now possible to cancel or go back to the previous step while selected columns are loading. 
  • Same print settings can now be applied for multiple reports in a single export. 
  • The "Manage Resources" tab has been removed from the the Plugin Manager.

What is new in version 7.6.1:

Bug fixes

  • Fixed an issue where some filtering operations, such as "doesn't contain" did not act correctly when filtering table cells that contained multiple pieces of information.
  • Fixed an issue where annotations that spanned the ends of a circular sequence would be incorrectly placed in the Circular Sequence View.
  • Fixed a bug that caused the workbench to freeze if certain sequences were displayed in circular view with radial rendering of labels.
  • Fixed an issue where some filtering operations, such as "doesn't contain" did not act correctly when filtering table cells that contained multiple pieces of information.
  • Fixed an issue that prevented a root folder on Windows drives from being used as a File Location.
  • Fixed an issue where updating an existing installation on Windows would result in the .vmoptions file being deleted, which makes the Workbench run with the default Java configuration.

What is new in version 7.6:

New features and improvements

  • A 3D Molecule Viewer is now available for visualization of protein, RNA, DNA, and small molecules.
  • Improved reporting of errors related to low disk space.

Bug fixes

  • Fixed problem with links and text in tables that were being cut off when succeeding a link.
  • Restriction site analysis: The values "Cut position(s)" column of the restriction site analysis table now behaves like numbers instead of text, meaning sorting and filtering works.
  • A problem with saved table settings that sometimes did not work has been fixed. The bug fix includes a more robust/generic way of saving table settings with different columns. To fix this problem, existing saved table settings should first be loaded on an object where it works (i.e. has the same columns as when it was saved); and then the table settings should be saved with the old name to overwrite the settings. 

  • Metadata for phylogenetic trees: A bug has been fixed with import of metadata containing column names with colons.

  • Fixed error when showing protein translations of annotations shorter than 3 bases.

What is new in version 7.5:

  • The unused "Workflows" button has been removed from the toolbar.
  • Local Search enabled from the menu bar now includes filtering on "Path".
  • Advanced filtering on tables now includes the option to filter for a space, comma or semi-colon delimited lists of terms.
  • Zoom tools redesign: The Zoom to selection feature is now also available for sequences, sequence lists, alignments, and read mappings.
  • Saving/applying side-panel settings for tables now works for different tables that share some columns. 
  • Copy operations can now be stopped.

  • Import of Example Data and imports done through dragging files into the workbench and dropping them in the Navigation Area will no longer block the user interface while executing. Instead, the import happens as a background process that can be monitored and controlled via the Processes tab in the lower left corner.

  • CLC workbenches now support high resolution displays such as Apple retina displays of all data shown in the View Area (including tooltips).
  • More informative naming of coding region translations produced by the tool Translate to Protein. The name for a coding region translation consists of the name of the input sequence followed by the annotation type and finally the annotation name.

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