Home » Release Notes » 4.1.0

Changes in version 4.1 (Nov 7, 2017)

New Functionality

  • Enhanced collections to support a folder view of the files.
  • Added support for formatting and updating code numbers for sequences stored in collections.
  • Provided the option of marking sequences in a collection as part of a "Working Set" that can be easily viewed and manipulated.
  • Added the ability to drag files from a collection in order to (a) copy them to another location or collection, (b) move them to the Trash, or (c) attach them to an email message.
  • Added an undoable "Trim History Tree" command to the pull-down menu at the top right of History view.
  • Added a "Batch Trim File Histories" command to the File menu.
    (Requested by Dan Piraner)
  • Added a new preference for automatically trimming the history of a sequence.
    (Suggested by Dan Piraner)
  • Added the ability to choose enzymes that are palindromic, uninterrupted
    (no internal N's), or nondegenerate (A, C, G, and T only) to the Choose Enzymes dialog.
    (Requested by Vadim Timerbaev)
  • Added the option to import only primers that have a unique binding site.
    (Requested by an anonymous customer)
  • Added absorbance values to the Properties tab for protein sequence files.
    (Requested by Genevieve Labbe)
  • Added an "Import from Another File" button to the "Edit References" dialog.
    (Suggested by Karl Brune)
  • Added "Date Created" as a sortable field when viewing a collection.
    (Requested by Seth Goldman)
  • Enabled drag and drop of entire folders into a collection, and added an "Import Folders into Collection" command.
  • Added a context menu to the Browse Common Features dialog's list to enable editing or removing a feature, adding or removing a feature from the Favorites list, or opening a feature in a new window.
  • Added a "Duplicate in New Window" button to the Browse Common Features dialog.
  • Added the ability to order constructs directly from Synbio Technologies.


  • Added support for multiple copies of the following qualifiers: allele, cell_line, cell_type, citation, clone, clone_lib, cultivar, dev_stage, experiment, function, host, isolate, lab_host, map, note, operon, PCR_conditions, phenotype, pop_variant, product, standard_name, strain, sub_clone, sub_strain, tissue_lib, tissue_type.
    (Requested by Novozymes)
  • Added an option in Preferences for hiding the dashed line tick marks in sequence traces.
    (Requested by Raffaele Fiorenza)
  • Reduced the minimum primer length for simulating mutagenesis.
    (Requested by Sriram Vijayraghavan)
  • Improved the import of multiple files of varying types into a collection.
    (Requested by Dan Kraut)
  • Added history colors for "Splice to Remove Introns".
  • Enhanced History view to display annealed oligo names.
  • Enhanced the Addgene importer so that when only a partial sequence is available, the topology is shown as linear, unless the backbone size is available, in which case a circular sequence padded with N's is shown.
  • Added the option of either preserving or updating the Date Added attribute when a file in collection is replaced by importing a new copy.
  • Ensured that after a common feature is edited, the list scrolls to show the edited feature if its name was modified.
  • Added "Swiss-Prot" to the list of formats offered when using Batch Convert File Format.
  • Made flipping a sequence trace an undoable action.
  • Added the option of requiring an exact match when replacing a feature name, primer name, or sequence author for sequences in a collection.
  • Added "Find Protein Sequence" and "Find Enzyme / Feature / Primer" commands to the Edit menu, by creating a cascading "Find" menu that improves discoverability.
  • Removed the compact format button from the side toolbar in the Anneal Oligos dialog because it provided minimal utility.
  • Added a warning to help prevent accidental pasting of a copied DNA sequence into the protein search controls.
  • Enhanced the Edit Feature dialog so that when using "Create Feature Segment", the list scrolls if necessary to make the created segment visible.
  • Added support for "Make Protein" from within the Browse Common Features dialog.
  • Added an alert when using a file with over 25 levels of ancestors, to indicate that simulations may be slow unless the history is trimmed.
  • Added a draggable splitter to the DNA feature dialogs to allow more space to view qualifier or segment information.
  • Added support for "New File From Selection" to the Simulate Agarose Gel dialog.
  • Made various optimizations.
  • Enhanced the color, alignment, and look and feel of buttons and other interface elements.
  • Reduced Linux download size.


  • Enhanced the GenBank importer to make better use of the SOURCE field.
    (Requested by Novozymes)
  • Enabled the import of malformed GenBank files that lack a LOCUS line.
    (Reported by Yoshihisa Oda)
  • Enhanced the reliability of the DNASTAR SeqBuilder and EditSeq importers.
    (Reported by Kensuke Kataoka and Alex Justen)
  • Improved the reliability of recognizing the default genetic code when opening DNASTAR SeqBuilder files.
    (Reported by Kensuke Kataoka)
  • Fixed an issue that prevented import of some Geneious files.
    (Reported by Karl)
  • Fixed an issue with decoding GenBank files saved by ApE where N's were encoded as *'s.
    (Reported by Bianca Nijmeijer)
  • Fixed an issue where remote recent files were sometimes not listed after quitting and starting the program.
    (Reported by Dr Fanny Passot)
  • Fixed an issue with importing some records from NCBI.
    (Reported by Thomas Folliard)
  • Improved the reliability of Undo/Redo after saving.
    (Reported by Leonid Valentovich)
  • Enabled the Copy command in the Save/Save As dialogs, while disabling other irrelevant menu commands.
    (Reported by David Scalzo)
  • Enabled use of the Copy keyboard shortcut from within the DNA feature dialogs.
    (Reported by Juan Antonio Raygoza Garay)
  • Fixed an issue with importing some sequences from Addgene.
    (Reported by Alexandra Iouranova)
  • Ensured that Sassafras-based installations will not consume a second license if a second copy of SnapGene is launched on the same computer.
  • Improved feature selection behavior so that when two overlapping features are selected, the union of the two feature sequences is selected.
  • Fixed the following unreliable shortcuts in cascading menus on macOS: File → Import → NCBI Sequence (Cmd+Shift+O) Edit → Copy Bottom Strand → 5'to 3' (Cmd+Shift+C)  Edit → Find → [Various]  View → Toolbars → Toggle [Top | Side] Toolbar  All Commercial (Cmd+Shift+Opt+A)  Nonredundant Commercial (Cmd+Opt+A)  Unique Cutters (Cmd+Opt+1)  Unique & Dual Cutters (Cmd+Opt+2)  6+ Cuters (Cmd+Opt+6)  Unique 6+ Cutters (Cmd+Opt+7)  Actions → Restriction Cloning → Insert One (Cmd+Opt+I)  Actions → OE PCR → Overlap Two (Cmd+Shift+D)  Tools → Align → Various
  • Fixed a number of memory leaks.
  • Made various stability improvements.
  • Fixed an issue where the "Save Changes" button was not always enabled when one or more files was selected while viewing "Unsaved" files.
  • Fixed an issue where history view did not clear when multiple files in a collection were selected.
  • Improved the process of assigning files imported into a collection to the correct area of the collection.
  • Fixed an issue with sorting collection files by date.
  • Fixed the macOS shortcut (Cmd+Backspace) discarding unsaved changes in Collections.
  • Fixed the macOS shortcut (Cmd+Backspace) closing a document without updating.
  • Edit → Select All and Edit → Invert Selection can now be used to select files in collections.
  • Ensured that feature directionality is preserved when exporting to GenBank format and re-importing.
  • Enabled the import of large Geneious files.
  • Disabled menu commands that should not be available in manipulation dialogs.
  • Removed nonfunctional SCF / ZTR / FASTQ options from the Batch Convert File Format dialog.
  • Fixed an issue where Edit → Find Protein Sequence could sometimes show the "Find Feature" controls instead while viewing a protein sequence.
  • Prevented a blue line from appearing inappropriately when clicking on the upper ruler in Sequence view.
  • Enabled the launch dialog to be closed on macOS even when it is configured to appear when all windows have been closed.
  • Modified the window announcing a new SnapGene version so that it no longer requires an immediate decision about updating.
  • Ensured that "Show Selected Features" and "Hide Selected Features" are properly enabled when interacting with protein sequences.
  • Fixed an issue where when importing multiple files into a collection, files could sometimes be shown in the wrong category.